How to filter a .bam file and keep the subjects

leorippel · 11-25-2016, 04:36 AM

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.

mastal · 11-25-2016, 06:33 AM

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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11-25-2016, 04:36 AM	#1
leorippel Junior Member Location: Brasil Join Date: Jan 2016 Posts: 1	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.

11-25-2016, 06:33 AM	#2
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 667	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.