Extract primary STAR mapped reads to specific chromosomes
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2.5 years ago
rubic ▴ 270

Hi,

I have RNA-seq reads which I mapped with STAR and I'd like to extract from the bam file the primary alignments that map to chr1, chr2, and chr3.

I know the second part is achieved by:

samtools view -b -L <my_chrs_bed_file> <my_bam_file>

So I'm mostly interested in the first part, and how to pipe the two parts.

Thanks

samtools STAR • 449 views
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I don't follow, what's the 'first' part you want to achieve? You have one question: how to extract reads aligning to chr1 chr2 etc, and you have the solution.

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