Using split/merge .bams for Cufflinks

[DerSeb]

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?

[vyellapa]

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

[zorph]

Yes, it works just be sure to sort.