Cufflinks On Chromosome 2

Question

[komal.rathi]

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?

Thanks

Answer 1

[Vivek]

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