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cellgeni / STARsolo

wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
GNU General Public License v3.0
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The problem of barcode prefix #11

Closed CCCBBG closed 2 months ago

CCCBBG commented 3 months ago

Excuse me.May I have a problem about barcode prefix

This is my bam format A00582:1096:HGLJCDSX7:2:2346:16179:25003 147 chr1 10001 3 41S108M1S = 0001 -108 AACCCTAACCATAACCCTAAACACACGTTTAAACCTAACCCTAAACCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT ,,,,,F:,,F,,:F,,:,,,,,,,:,,,,F,F,,,FF:FF,,,FFF,,,FF,,,,:FF,F,FFF,F,F,F::FFFF:,FFF:,FFFFFF:FFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:2 HI:i:1 AS:i:206 nM:i:3 XS:Z:Unassigned_NoFeatures CB:Z:S001_ATCGATGATGCCC CR:Z:S001_ATCGATGATGCCTAACC UB:Z:CTAACCCTAACC UR:Z:CTAACCCTAACC

I have changed the general bam format such as CB CR My parameters were --soloInputSAMattrBarcodeSeq CB UB \ --soloCBwhitelist None \ --soloCBlen 22 \ --soloUMIlen 12 \ --soloFeatures Gene SJ \ --soloBarcodeReadLength 0 \ --soloStrand Reverse

But it seems to be an error It occurs to me in Log.out that Finished reading reads from Solo files nCB=0, nReadPerCBmax=0, nMatch=0

What's going on? I am looking forward to your reply.Thank you very much

apredeus commented 2 months ago

Hi @CCCBBG ,

Unfortunately, I have no idea what are you trying to achieve. This repository is for STARsolo mapping/quantification, which usually starts from fastq files. Are you trying to start from a BAM file? What are you trying to do in general?