Extract primary STAR mapped reads to specific chromosomes

Question

[rubic]

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

[Mark]

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.