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fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
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FilterConsensusReads results too little reads compared raw fastq OR uBAM file #990

Open teryyoung opened 3 months ago

teryyoung commented 3 months ago

hello, I runned fgbio's FilterConsensusReads to my RNAseq data, but the output results files are of too little size. The raw read uBAM file had 3-4GB, after first mapping and quality control, there had 2GB data, this is one of the tag family size histogram file. image

my issue is this, after I CallConsensusReads and FilterConsensusReads, is seems most of reads were filtered out, just 38kB data

I tried increase the umi from 5 to 6, and it didn't work, if someone know how to sovle this problem?