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Old 11-25-2016, 04:36 AM   #1
leorippel
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Default How to filter a .bam file and keep the subjects

Hello All,

I have multiple alignments generated to DEG analysis. I know that grep for unaligned reads is not trust and the best way is the -f4 flag. But here what I want is the contigs with no alignment with those reds from specific libraries.

I already have the counts matrices and I can grep those sequences from the matrix, but I want to do a sanity check .


Thank's in advanced.
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Old 11-25-2016, 06:33 AM   #2
mastal
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Samtools idxstats should give you a list of how many reads aligned to each of the contigs in your reference genome, i.e. the sequences that are listed in the sam/bam headers.
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