read counts per chromosome arm
I have DNAseq data and trying to get the read counts per chromosome arm. but I do not know the correct way. shall I align to every chromosome separately or the whole genome? how can I count the reads per chromosome arm? I mean what tool can I use for this goal?
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Pierre Lindenbaum
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Sara
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Sara
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get a bed for each q/p for each chromosome, eg. see Programmatically convert cytoband location to genomic coordinates
then for each bed record, use samtools view -c to count the reads.
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