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?
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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