Question: Cufflinks On Chromosome 2
gravatar for komal.rathi
6.5 years ago by
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.6k wrote:

Hello everyone,

I have a sorted and index BAM file. I want to run cufflinks on just Chromosome2 from it to save time. How can I do it?

I was using:

cufflinks -p 2 -g <chr2 filtered GTF file> -o outputdir input_filter_sort.bam 2> input.out

I dont know whether this is the best way to do it. I also want to assemble novel transcripts along with the known ones on chromosome2 so I am using the -g option instead of -G. But this command assembles novel transcripts on all the chromosomes not just on chromosome 2. Is there a way to assemble known and novel transcripts on just one chromosome?


cufflinks • 1.8k views
ADD COMMENTlink modified 6.5 years ago by Vivek2.4k • written 6.5 years ago by komal.rathi3.6k
gravatar for Vivek
6.5 years ago by
Vivek2.4k wrote:

You can use samtools to just extract chromosome 2 from your bam and use cufflinks on it.

samtools view -bh allChr.bam chr2 > onlyChr2.bam
ADD COMMENTlink written 6.5 years ago by Vivek2.4k
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