Using split/merge .bams for Cufflinks

DerSeb

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#1

Using split/merge .bams for Cufflinks

01-13-2011, 12:31 PM

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?
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vyellapa

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01-24-2012, 06:44 PM

did samtools or picard succeed in merging the bams so that they could be used as input for cufflinks?
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zorph

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03-15-2012, 10:42 AM

Yes, it works just be sure to sort.
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