Updated documentation.

jfjlaros · Mar 10, 2021 · 49ac1e5 · 49ac1e5
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diff --git a/README.rst b/README.rst
@@ -27,9 +27,11 @@ Demultiplex: FASTA/FASTQ demultiplexer
 Versatile NGS demultiplexer with the following features:
 
 - Support for FASTA and FASTQ files.
+- Support for gzip and bzip2 compressed files.
 - Support for multiple reads per fragment, e.g., paired-end.
 - Handles barcodes in the header and in the reads.
-- Handles barcodes at *unknown* locations in reads (e.g., PacBio or Nanopore barcodes).
+- Handles barcodes at *unknown* locations in reads (e.g., PacBio or Nanopore
+  barcodes).
 - Support for selection of part of a barcode.
 - Allows for mismatches, insertions and deletions.
 - Barcode guessing by frequency or fixed amount.

diff --git a/data/demultiplex.fq.bz2 b/data/demultiplex.fq.bz2
diff --git a/data/demultiplex.fq.gz b/data/demultiplex.fq.gz
diff --git a/docs/faq.rst b/docs/faq.rst
@@ -0,0 +1,45 @@
+Frequently asked questions
+==========================
+
+Can this program work with dual barcodes / indexes?
+
+    Yes, but not directly. Because of the large amount of dual (or more)
+    indexing approaches, the user interface would become incomprehensible. This
+    is why we have decided to support only the basic cases. In order to support
+    an arbitrary amount of barcodes see Section :ref:`multiple_barcodes`.
+
+
+Can you add support for removing barcodes after demultiplexing?
+
+    We used to have this type of functionality (selecting parts of a read) in a
+    previous version, but because of the large number of complicated barcoding
+    schemas (multiple barcodes in one read, barcodes in multiple reads, etc.),
+    we found that this interface was not flexible enough. Instead, we recommend
+    to use a more generic tool for post processing the demultiplexed files, The
+    Fastools_ ``select`` command for example.
+
+
+My sequencing run was pretty bad, can / should I increase the number of allowed
+mismatches?
+
+    It depends on which barcodes were used. Most barcode sets are designed to
+    allow for single nucleotide read errors. When multiple errors occur, it may
+    not be possible to uniquely assign a read to a barcode. You can use the
+    Barcode_ ``test`` command to see if your barcode set allows for multiple
+    error correction.
+
+
+I do not know which / how many barcodes were used. How can I demultiplex my
+file?
+
+    The best thing to do is to contact your sequencing provider and ask which
+    barcodes were used. If this is not possible for some reason, you may want
+    to ``guess`` subcommand described in Section :ref:`illumina`. If the
+    barcodes are in the read instead of the header, you may want to use a tool
+    like FastQC_ to find overrepresented sequences. These may be the barcodes
+    you are looking for.
+
+
+.. _FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+.. _Fastools: https://fastools.readthedocs.io/
+.. _Barcode: https://barcode.readthedocs.io/
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,5 +6,5 @@
 
    installation
    usage
-   library
+   faq
    credits
diff --git a/docs/library.rst b/docs/library.rst
diff --git a/docs/usage.rst b/docs/usage.rst
@@ -22,6 +22,7 @@ that particular subcommand. For example:
 
     demultiplex demux -h
 
+.. _illumina:
 
 Illumina FASTQ files
 --------------------
@@ -148,6 +149,8 @@ command:
     demultiplex demux -r -e 6 barcodes.csv file.fq
 
 
+.. _multiple_barcodes:
+
 Multiple barcodes
 -----------------