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How to perform corrected Cell Barcode/UMI calling with an externally sorted BAM? #2241

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mkarikom opened this issue Nov 14, 2024 · 0 comments

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@mkarikom
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I require Cell Barcode / UMI calling but am unable to sort BAMs within STARsolo due to a limited system RAM.
When I set limitBAMsortRAM==<ammount of RAM on my system>, STAR throws the following error:

EXITING because of fatal ERROR: not enough memory for BAM sorting: 
SOLUTION: re-run STAR with at least --limitBAMsortRAM 273246110398 

Proposed solution:

  1. Run STARsolo with
  2. run samtools sort with my hard memory limits as follows:
samtools sort -m ${BAMSORTRAM} -@ ${BAMSORTNTHREADS} -o "${base}_STARsolo/${base}_Aligned.sortedByCoord.out.bam" "${base}_STARsolo/${base}_Aligned.out.bam"

So how do I re-run STARsolo just to call Barcodes/UMIS on:

  1. the original alignment (which produced the unsorted BAM subsequently aligned with samtools above) and the subsequently sorted BAM
  2. the sorted BAM from samtools (command shown above)
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