Question: read counts per chromosome arm
gravatar for Sara
13 months ago by
Sara90 wrote:

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?

alignment genome • 243 views
ADD COMMENTlink modified 13 months ago by Pierre Lindenbaum129k • written 13 months ago by Sara90
gravatar for Pierre Lindenbaum
13 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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.

ADD COMMENTlink written 13 months ago by Pierre Lindenbaum129k
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