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?