[edge]

Thanks chadn737,
In order to run Cufflink in default, is it I must include or exclude "-h" option?
eg.

samtools view input.bam > output.sam

Thanks again.

[reut]

you can run cufflinks with the .bam file

Thanks chadn737,
In order to run Cufflink in default, is it I must include or exclude "-h" option?
eg.

samtools view input.bam > output.sam

Thanks again.

You don't have to convert the accepted_hits.bam to .sam for cufflinks, it works with the bam file as well.
(which is better, since the bam file is compressed and therefore a lot smaller than the sam file)