Linux command line problem #1
Comments
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Hello,
I think you are missing the fourth argument that is the number of
processors. This argument is just for doing multiprocessing. If you don't
want to use multiple processors, you can type 1 as the fourth argument in
the command line.
If you have any questions, please let me know.
Best wishes
Catherine
…On 4 April 2017 at 13:33, gwaldbieser ***@***.***> wrote:
Thanks for this program! I would prefer to use the Linux command line so
that I don't have to transfer fastq files to a Windows machine. I am trying
to run the test data on Linux but cannot get the command line to accept the
inputs, even when using full path information. I have unzipped the test
fastq files and renamed the folder to JGPedigree_Fastq (to remove spaces).
(From within /mnt/data8/MegasatTestData/)
$perl /home/software/MEGASAT/MEGASAT_Genotype.pl
/mnt/data8/MegasatTestData/primer-input.txt 2 5
/mnt/data8/MegasatTestData/Pedigree/JGPedigree_Fastq/
/mnt/data8/MegasatTestData/output
Missing command line arguments!
#######################################################################
Need the directory of primer file as the first command-line argument
Need the maximum number of mismatches as the second command-line argument
Need the minimum depth threshold as the third command-line argument
Need the directory of data set folder that contains all the input sequence
read files (fastq or fasta) as the fourth command-line argument
Need the directory to save the output folder as the fifth command-line
argument
I would appreciate if you would you provide more detail on the expected
inputs for the command line.
Geoff
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Ah, that makes sense now in light of the parameters entered in the Windows GUI but it wasn't obvious in the error messaging. It's working now. |
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Initially, I ran the test data which worked as expected. When I tested some of my data only blank genotypes were output. I tracked it down to an error on page 6 of the User's Manual where the column labels for 5' flank and 3' flank were switched. Once I switched those columns in my primer file then everything worked well. |
|
Thank you for telling me this error in the User's Manual. I didn't notice
before. I will change it to the correct format. Thank you.
Best wishes
Catherine
…On 5 April 2017 at 11:33, gwaldbieser ***@***.***> wrote:
Initially, I ran the test data which worked as expected. When I tested
some of my data only blank genotypes were output. I tracked it down to an
error on page 6 of the User's Manual where the column labels for 5' flank
and 3' flank were switched. Once I switched those columns in my primer file
then everything worked well.
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I have looked at the manuscript online and supplemental material and cannot find details on the scoring rules and how the six scoring ratios are defined. Can you provide that information, please? |
|
I think we provided the scoring information in the supplemental material.
Anyway, I just found a word file (attached) that explains the scoring
rules. If you have any questions, please let me know.
Thank you!
Best wishes
Catherine
…On 5 April 2017 at 13:05, gwaldbieser ***@***.***> wrote:
I have looked at the manuscript online and supplemental material and
cannot find details on the scoring rules and how the six scoring ratios are
defined. Can you provide that information, please?
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Hi Catherine, |
|
Hi Geoff,
Could you send me your email address? I can attach that word file in the
email.
Best wishes
Catherine
…On 5 April 2017 at 13:36, gwaldbieser ***@***.***> wrote:
Hi Catherine,
I couldn't find it in the supporting information online (Appendices S1-S4).
The MS Word file did not attach. Can you post it to the code page?
Thanks.
Geoff
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Thanks! |
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Hi Catherine,
When using MEGASAT, does the MRA have to be a perfect repeat?
Geoff
From: CatherineZhan [mailto:[email protected]]
Sent: Wednesday, April 05, 2017 11:42 AM
To: beiko-lab/MEGASAT <[email protected]>
Cc: Waldbieser, Geoff <[email protected]>; Author <[email protected]>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Geoff,
Could you send me your email address? I can attach that word file in the
email.
Best wishes
Catherine
On 5 April 2017 at 13:36, gwaldbieser ***@***.******@***.***>> wrote:
Hi Catherine,
I couldn't find it in the supporting information online (Appendices S1-S4).
The MS Word file did not attach. Can you post it to the code page?
Thanks.
Geoff
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Hi Geoff,
The MRA does not need to be perfect repeat. We allow sequencing errors in
that repeating area.
Thank you.
Best wishes
Catherine
…On 10 May 2017 at 18:33, gwaldbieser ***@***.***> wrote:
Hi Catherine,
When using MEGASAT, does the MRA have to be a perfect repeat?
Geoff
From: CatherineZhan ***@***.***
Sent: Wednesday, April 05, 2017 11:42 AM
To: beiko-lab/MEGASAT ***@***.***>
Cc: Waldbieser, Geoff ***@***.***>; Author <
***@***.***>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Geoff,
Could you send me your email address? I can attach that word file in the
email.
Best wishes
Catherine
On 5 April 2017 at 13:36, gwaldbieser ***@***.***<mailto:
***@***.***>> wrote:
> Hi Catherine,
> I couldn't find it in the supporting information online (Appendices
S1-S4).
> The MS Word file did not attach. Can you post it to the code page?
> Thanks.
> Geoff
>
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Thanks. I’m trying to track down why some new loci worked and some did not. It must be somewhere in the sequence I selected for the primer file.
Does the FF sequence need to include all sequence between the FP and MRA? Likewise, does the RF sequence need to include everything from the MRA to the RP?
From: CatherineZhan [mailto:[email protected]]
Sent: Thursday, May 11, 2017 6:29 AM
To: beiko-lab/MEGASAT <[email protected]>
Cc: Waldbieser, Geoff <[email protected]>; Author <[email protected]>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Geoff,
The MRA does not need to be perfect repeat. We allow sequencing errors in
that repeating area.
Thank you.
Best wishes
Catherine
On 10 May 2017 at 18:33, gwaldbieser ***@***.******@***.***>> wrote:
Hi Catherine,
When using MEGASAT, does the MRA have to be a perfect repeat?
Geoff
From: CatherineZhan ***@***.***
Sent: Wednesday, April 05, 2017 11:42 AM
To: beiko-lab/MEGASAT ***@***.******@***.***>>
Cc: Waldbieser, Geoff ***@***.******@***.***>>; Author <
***@***.******@***.***>>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Geoff,
Could you send me your email address? I can attach that word file in the
email.
Best wishes
Catherine
On 5 April 2017 at 13:36, gwaldbieser ***@***.***<mailto:
> Hi Catherine,
> I couldn't find it in the supporting information online (Appendices
S1-S4).
> The MS Word file did not attach. Can you post it to the code page?
> Thanks.
> Geoff
>
> —
> You are receiving this because you commented.
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> <#1 (comment)>,
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Yes, the FF will be the sequence between FP and the MRA. Likewise, the RF
will be the sequence between the MRA and RP.
Catherine
…On 11 May 2017 at 10:17, gwaldbieser ***@***.***> wrote:
Thanks. I’m trying to track down why some new loci worked and some did
not. It must be somewhere in the sequence I selected for the primer file.
Does the FF sequence need to include all sequence between the FP and MRA?
Likewise, does the RF sequence need to include everything from the MRA to
the RP?
From: CatherineZhan ***@***.***
Sent: Thursday, May 11, 2017 6:29 AM
To: beiko-lab/MEGASAT ***@***.***>
Cc: Waldbieser, Geoff ***@***.***>; Author <
***@***.***>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Geoff,
The MRA does not need to be perfect repeat. We allow sequencing errors in
that repeating area.
Thank you.
Best wishes
Catherine
On 10 May 2017 at 18:33, gwaldbieser ***@***.***<mailto:
***@***.***>> wrote:
> Hi Catherine,
> When using MEGASAT, does the MRA have to be a perfect repeat?
>
> Geoff
>
> From: CatherineZhan ***@***.***
> Sent: Wednesday, April 05, 2017 11:42 AM
> To: beiko-lab/MEGASAT ***@***.***<mailto:
***@***.***>>
> Cc: Waldbieser, Geoff ***@***.***<mailto:
***@***.***>>; Author <
> ***@***.******@***.***>>
> Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
>
> Hi Geoff,
>
> Could you send me your email address? I can attach that word file in the
> email.
>
> Best wishes
> Catherine
>
> On 5 April 2017 at 13:36, gwaldbieser ***@***.***<mailto:
***@***.***%3cmailto:%0b>> ***@***.***<
***@***.***>>> wrote:
>
> > Hi Catherine,
> > I couldn't find it in the supporting information online (Appendices
> S1-S4).
> > The MS Word file did not attach. Can you post it to the code page?
> > Thanks.
> > Geoff
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#1 (comment)>,
> > or mute the thread
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> >
>
>
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The entire sequence? It seems that if I skip some bases between the FP and FF sequences then the genotypes don’t get called, but if I only use ‘X’ for the FF then the genotypes are called. My question is – does the entire 5’ flanking sequence on the input reads need to be accounted for by the FP and FF sequences?
From: CatherineZhan [mailto:[email protected]]
Sent: Thursday, May 11, 2017 8:56 AM
To: beiko-lab/MEGASAT <[email protected]>
Cc: Waldbieser, Geoff <[email protected]>; Author <[email protected]>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Yes, the FF will be the sequence between FP and the MRA. Likewise, the RF
will be the sequence between the MRA and RP.
Catherine
On 11 May 2017 at 10:17, gwaldbieser ***@***.******@***.***>> wrote:
Thanks. I’m trying to track down why some new loci worked and some did
not. It must be somewhere in the sequence I selected for the primer file.
Does the FF sequence need to include all sequence between the FP and MRA?
Likewise, does the RF sequence need to include everything from the MRA to
the RP?
From: CatherineZhan ***@***.***
Sent: Thursday, May 11, 2017 6:29 AM
To: beiko-lab/MEGASAT ***@***.******@***.***>>
Cc: Waldbieser, Geoff ***@***.******@***.***>>; Author <
***@***.******@***.***>>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Geoff,
The MRA does not need to be perfect repeat. We allow sequencing errors in
that repeating area.
Thank you.
Best wishes
Catherine
On 10 May 2017 at 18:33, gwaldbieser ***@***.***<mailto:
> Hi Catherine,
> When using MEGASAT, does the MRA have to be a perfect repeat?
>
> Geoff
>
> From: CatherineZhan ***@***.***
> Sent: Wednesday, April 05, 2017 11:42 AM
> To: beiko-lab/MEGASAT ***@***.***<mailto:
> Cc: Waldbieser, Geoff ***@***.***<mailto:
> ***@***.******@***.******@***.******@***.***>>>
> Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
>
> Hi Geoff,
>
> Could you send me your email address? I can attach that word file in the
> email.
>
> Best wishes
> Catherine
>
> On 5 April 2017 at 13:36, gwaldbieser ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>> [email protected]<<mailto:[email protected]%3c>
***@***.***>>> wrote:
>
> > Hi Catherine,
> > I couldn't find it in the supporting information online (Appendices
> S1-S4).
> > The MS Word file did not attach. Can you post it to the code page?
> > Thanks.
> > Geoff
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <#1 (comment)>,
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> >
>
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The reason why the genotypes are called when using "X" for the FF is
because script will assume the locus does not have FF and search for the
other components. In some cases, if you skip some bases between FP and FF,
the genotypes should be called. I would suggest you to include the entire
sequence for FF and RF.
Catherine
…On 11 May 2017 at 10:59, gwaldbieser ***@***.***> wrote:
The entire sequence? It seems that if I skip some bases between the FP and
FF sequences then the genotypes don’t get called, but if I only use ‘X’ for
the FF then the genotypes are called. My question is – does the entire 5’
flanking sequence on the input reads need to be accounted for by the FP and
FF sequences?
From: CatherineZhan ***@***.***
Sent: Thursday, May 11, 2017 8:56 AM
To: beiko-lab/MEGASAT ***@***.***>
Cc: Waldbieser, Geoff ***@***.***>; Author <
***@***.***>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Yes, the FF will be the sequence between FP and the MRA. Likewise, the RF
will be the sequence between the MRA and RP.
Catherine
On 11 May 2017 at 10:17, gwaldbieser ***@***.***<mailto:
***@***.***>> wrote:
> Thanks. I’m trying to track down why some new loci worked and some did
> not. It must be somewhere in the sequence I selected for the primer
file.
> Does the FF sequence need to include all sequence between the FP and
MRA?
> Likewise, does the RF sequence need to include everything from the MRA
to
> the RP?
>
> From: CatherineZhan ***@***.***
> Sent: Thursday, May 11, 2017 6:29 AM
> To: beiko-lab/MEGASAT ***@***.***<mailto:
***@***.***>>
> Cc: Waldbieser, Geoff ***@***.***<mailto:
***@***.***>>; Author <
> ***@***.******@***.***>>
> Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
>
> Hi Geoff,
>
> The MRA does not need to be perfect repeat. We allow sequencing errors
in
> that repeating area.
>
> Thank you.
>
> Best wishes
> Catherine
>
>
> On 10 May 2017 at 18:33, gwaldbieser ***@***.***<mailto:
***@***.***%3cmailto:%0b>> ***@***.***<
***@***.***>>> wrote:
>
> > Hi Catherine,
> > When using MEGASAT, does the MRA have to be a perfect repeat?
> >
> > Geoff
> >
> > From: CatherineZhan ***@***.***
> > Sent: Wednesday, April 05, 2017 11:42 AM
> > To: beiko-lab/MEGASAT ***@***.***<mailto:
***@***.***%3cmailto:%0b>>
***@***.******@***.***>>>
> > Cc: Waldbieser, Geoff ***@***.***<mailto:
***@***.***%3cmailto:%0b>>
***@***.******@***.***>>>;
Author <
> > ***@***.******@***.***<mailto:
***@***.******@***.***>>>
> > Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
> >
> > Hi Geoff,
> >
> > Could you send me your email address? I can attach that word file in
the
> > email.
> >
> > Best wishes
> > Catherine
> >
> > On 5 April 2017 at 13:36, gwaldbieser ***@***.***<
mailto:
***@***.***%3cmailto:%0b>> <mailto:
***@***.***%3cmailto:%0b>> ***@***.***<<mailto:
***@***.***%3c>
> ***@***.***>>> wrote:
> >
> > > Hi Catherine,
> > > I couldn't find it in the supporting information online (Appendices
> > S1-S4).
> > > The MS Word file did not attach. Can you post it to the code page?
> > > Thanks.
> > > Geoff
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <#1 (comment)-
291920098>,
>
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/
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> > > .
> > >
> >
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Hi Catherine,
I am wondering why the sometimes the algorithm identifies two major allele counts but calls only one allele in the genotype. This happens in a locus that has a very large number of alleles. Here are examples where I used the default basecall settings in the primer file.
Name left_oligo Rev_Comp_right_oligo 5Flank 3Flank Repeat
c19-02 CCTACGATTAGTGGACAACCCGCTCTACCACCTGAGCCACAGCTG TAGTGAAAGCCCAGTTCGGTG X ACCCACAGCAGCAGT GATA
Here are results in the length distribution file ( I have removed columns with zero reads).
Microsatellite
39
85
111
127
133
136
137
141
157
169
171
175
183
187
195
199
217
221
225
229
233
sum
scores
c19-02
2
1
1
1
7
1
227
1
1
3
1
8
1
8
1
1
1
24
454
4
3
751
225 225
Microsatellite
77
111
133
137
141
169
175
177
187
191
217
221
224
225
229
253
sum
scores
c19-02
1
1
14
297
1
2
2
1
11
1
1
16
1
571
5
1
926
225 225
Why were these samples not be genotyped as 137/225?
Geoff
From: CatherineZhan [mailto:[email protected]]
Sent: Thursday, May 11, 2017 9:09 AM
To: beiko-lab/MEGASAT <[email protected]>
Cc: Waldbieser, Geoff <[email protected]>; Author <[email protected]>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
The reason why the genotypes are called when using "X" for the FF is
because script will assume the locus does not have FF and search for the
other components. In some cases, if you skip some bases between FP and FF,
the genotypes should be called. I would suggest you to include the entire
sequence for FF and RF.
Catherine
On 11 May 2017 at 10:59, gwaldbieser ***@***.******@***.***>> wrote:
The entire sequence? It seems that if I skip some bases between the FP and
FF sequences then the genotypes don’t get called, but if I only use ‘X’ for
the FF then the genotypes are called. My question is – does the entire 5’
flanking sequence on the input reads need to be accounted for by the FP and
FF sequences?
From: CatherineZhan ***@***.***
Sent: Thursday, May 11, 2017 8:56 AM
To: beiko-lab/MEGASAT ***@***.******@***.***>>
Cc: Waldbieser, Geoff ***@***.******@***.***>>; Author <
***@***.******@***.***>>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Yes, the FF will be the sequence between FP and the MRA. Likewise, the RF
will be the sequence between the MRA and RP.
Catherine
On 11 May 2017 at 10:17, gwaldbieser ***@***.***<mailto:
> Thanks. I’m trying to track down why some new loci worked and some did
> not. It must be somewhere in the sequence I selected for the primer
file.
> Does the FF sequence need to include all sequence between the FP and
MRA?
> Likewise, does the RF sequence need to include everything from the MRA
to
> the RP?
>
> From: CatherineZhan ***@***.***
> Sent: Thursday, May 11, 2017 6:29 AM
> To: beiko-lab/MEGASAT ***@***.***<mailto:
> Cc: Waldbieser, Geoff ***@***.***<mailto:
> ***@***.******@***.******@***.******@***.***>>>
> Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
>
> Hi Geoff,
>
> The MRA does not need to be perfect repeat. We allow sequencing errors
in
> that repeating area.
>
> Thank you.
>
> Best wishes
> Catherine
>
>
> On 10 May 2017 at 18:33, gwaldbieser ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>> [email protected]<<mailto:[email protected]%3c>
***@***.***>>> wrote:
>
> > Hi Catherine,
> > When using MEGASAT, does the MRA have to be a perfect repeat?
> >
> > Geoff
> >
> > From: CatherineZhan ***@***.***
> > Sent: Wednesday, April 05, 2017 11:42 AM
> > To: beiko-lab/MEGASAT ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>>
***@***.******@***.******@***.******@***.***>>>>
> > Cc: Waldbieser, Geoff ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>>
***@***.******@***.******@***.******@***.***>>>>;
Author <
> > ***@***.******@***.******@***.******@***.***%3cmailto>:
***@***.******@***.******@***.******@***.***>>>>
> > Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
> >
> > Hi Geoff,
> >
> > Could you send me your email address? I can attach that word file in
the
> > email.
> >
> > Best wishes
> > Catherine
> >
> > On 5 April 2017 at 13:36, gwaldbieser ***@***.***<
<mailto:[email protected]%3c%0b>> mailto:
***@***.***%3cmailto:%0b>> <mailto:
<mailto:%0b>> [email protected]%3cmailto:%0b<mailto:[email protected]%3cmailto:%0b>>> [email protected]<<mailto<mailto:[email protected]%3c%3cmailto>:
***@***.******@***.***%3c>>
> ***@***.***>>> wrote:
> >
> > > Hi Catherine,
> > > I couldn't find it in the supporting information online (Appendices
> > S1-S4).
> > > The MS Word file did not attach. Can you post it to the code page?
> > > Thanks.
> > > Geoff
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <#1 (comment)-
291920098>,
>
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I think I see it now. A1>A2 and A2/A1 is less than R4 (default value=0.6)?
From: Waldbieser, Geoff
Sent: Friday, June 09, 2017 11:21 AM
To: 'beiko-lab/MEGASAT' <[email protected]>
Subject: RE: [beiko-lab/MEGASAT] Linux command line problem (#1)
Hi Catherine,
I am wondering why the sometimes the algorithm identifies two major allele counts but calls only one allele in the genotype. This happens in a locus that has a very large number of alleles. Here are examples where I used the default basecall settings in the primer file.
Name left_oligo Rev_Comp_right_oligo 5Flank 3Flank Repeat
c19-02 CCTACGATTAGTGGACAACCCGCTCTACCACCTGAGCCACAGCTG TAGTGAAAGCCCAGTTCGGTG X ACCCACAGCAGCAGT GATA
Here are results in the length distribution file ( I have removed columns with zero reads).
Microsatellite
39
85
111
127
133
136
137
141
157
169
171
175
183
187
195
199
217
221
225
229
233
sum
scores
c19-02
2
1
1
1
7
1
227
1
1
3
1
8
1
8
1
1
1
24
454
4
3
751
225 225
Microsatellite
77
111
133
137
141
169
175
177
187
191
217
221
224
225
229
253
sum
scores
c19-02
1
1
14
297
1
2
2
1
11
1
1
16
1
571
5
1
926
225 225
Why were these samples not be genotyped as 137/225?
Geoff
From: CatherineZhan [mailto:[email protected]]
Sent: Thursday, May 11, 2017 9:09 AM
To: beiko-lab/MEGASAT <[email protected]<mailto:[email protected]>>
Cc: Waldbieser, Geoff <[email protected]<mailto:[email protected]>>; Author <[email protected]<mailto:[email protected]>>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
The reason why the genotypes are called when using "X" for the FF is
because script will assume the locus does not have FF and search for the
other components. In some cases, if you skip some bases between FP and FF,
the genotypes should be called. I would suggest you to include the entire
sequence for FF and RF.
Catherine
On 11 May 2017 at 10:59, gwaldbieser ***@***.******@***.***>> wrote:
The entire sequence? It seems that if I skip some bases between the FP and
FF sequences then the genotypes don’t get called, but if I only use ‘X’ for
the FF then the genotypes are called. My question is – does the entire 5’
flanking sequence on the input reads need to be accounted for by the FP and
FF sequences?
From: CatherineZhan ***@***.***
Sent: Thursday, May 11, 2017 8:56 AM
To: beiko-lab/MEGASAT ***@***.******@***.***>>
Cc: Waldbieser, Geoff ***@***.******@***.***>>; Author <
***@***.******@***.***>>
Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
Yes, the FF will be the sequence between FP and the MRA. Likewise, the RF
will be the sequence between the MRA and RP.
Catherine
On 11 May 2017 at 10:17, gwaldbieser ***@***.***<mailto:
> Thanks. I’m trying to track down why some new loci worked and some did
> not. It must be somewhere in the sequence I selected for the primer
file.
> Does the FF sequence need to include all sequence between the FP and
MRA?
> Likewise, does the RF sequence need to include everything from the MRA
to
> the RP?
>
> From: CatherineZhan ***@***.***
> Sent: Thursday, May 11, 2017 6:29 AM
> To: beiko-lab/MEGASAT ***@***.***<mailto:
> Cc: Waldbieser, Geoff ***@***.***<mailto:
> ***@***.******@***.******@***.******@***.***>>>
> Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
>
> Hi Geoff,
>
> The MRA does not need to be perfect repeat. We allow sequencing errors
in
> that repeating area.
>
> Thank you.
>
> Best wishes
> Catherine
>
>
> On 10 May 2017 at 18:33, gwaldbieser ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>> [email protected]<<mailto:[email protected]%3c>
***@***.***>>> wrote:
>
> > Hi Catherine,
> > When using MEGASAT, does the MRA have to be a perfect repeat?
> >
> > Geoff
> >
> > From: CatherineZhan ***@***.***
> > Sent: Wednesday, April 05, 2017 11:42 AM
> > To: beiko-lab/MEGASAT ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>>
***@***.******@***.******@***.******@***.***>>>>
> > Cc: Waldbieser, Geoff ***@***.***<mailto:
<mailto:[email protected]%3cmailto:%0b>> <mailto:[email protected]%3cmailto:%0b>>
***@***.******@***.******@***.******@***.***>>>>;
Author <
> > ***@***.******@***.******@***.******@***.***%3cmailto>:
***@***.******@***.******@***.******@***.***>>>>
> > Subject: Re: [beiko-lab/MEGASAT] Linux command line problem (#1)
> >
> > Hi Geoff,
> >
> > Could you send me your email address? I can attach that word file in
the
> > email.
> >
> > Best wishes
> > Catherine
> >
> > On 5 April 2017 at 13:36, gwaldbieser ***@***.***<
<mailto:[email protected]%3c%0b>> mailto:
***@***.***%3cmailto:%0b>> <mailto:
<mailto:%0b>> [email protected]%3cmailto:%0b<mailto:[email protected]%3cmailto:%0b>>> [email protected]<<mailto<mailto:[email protected]%3c%3cmailto>:
***@***.******@***.***%3c>>
> ***@***.***>>> wrote:
> >
> > > Hi Catherine,
> > > I couldn't find it in the supporting information online (Appendices
> > S1-S4).
> > > The MS Word file did not attach. Can you post it to the code page?
> > > Thanks.
> > > Geoff
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <#1 (comment)-
291920098>,
>
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Thanks for this program! I would prefer to use the Linux command line so that I don't have to transfer fastq files to a Windows machine. I am trying to run the test data on Linux but cannot get the command line to accept the inputs, even when using full path information. I have unzipped the test fastq files and renamed the folder to JGPedigree_Fastq (to remove spaces).
(From within /mnt/data8/MegasatTestData/)
$perl /home/software/MEGASAT/MEGASAT_Genotype.pl /mnt/data8/MegasatTestData/primer-input.txt 2 5 /mnt/data8/MegasatTestData/Pedigree/JGPedigree_Fastq/ /mnt/data8/MegasatTestData/output
Missing command line arguments!
#######################################################################
Need the directory of primer file as the first command-line argument
Need the maximum number of mismatches as the second command-line argument
Need the minimum depth threshold as the third command-line argument
Need the directory of data set folder that contains all the input sequence read files (fastq or fasta) as the fourth command-line argument
Need the directory to save the output folder as the fifth command-line argument
I would appreciate if you would you provide more detail on the expected inputs for the command line.
Geoff
The text was updated successfully, but these errors were encountered: