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Old 01-13-2011, 11:31 AM   #1
Location: Singapore

Join Date: Oct 2009
Posts: 44
Default Using split/merge .bams for Cufflinks

Dear all,

today I have a question regarding splitting and merging of .bam files as input for cufflinks.

For speeding up my calculations and trying different parameters, I have split and merged .bam files using samtools merge and samtools view.

When bam files are split into different chromosomes and each chromosome is analyzed independently, can I afterwards combine the cufflinks output and compare the information?

I ask this, since the header in the .bam file still has information about all the chromosomes in the previous files. Does this effect the FPKM tracking?
DerSeb is offline   Reply With Quote
Old 01-24-2012, 05:44 PM   #2
Location: phoenix

Join Date: Oct 2011
Posts: 59

did samtools or picard succeed in merging the bams so that they could be used as input for cufflinks?
vyellapa is offline   Reply With Quote
Old 03-15-2012, 10:42 AM   #3
Location: FL

Join Date: May 2010
Posts: 40

Yes, it works just be sure to sort.
zorph is offline   Reply With Quote

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