This question has been asked here previously: http://seqanswers.com/forums/showthr...s+preprocessed
Similarly, I have trimmed, aligned and sorted using STAR, add read groups, and marked duplicates to my BAM file. I'm curious if this processed BAM file is suitable for input into Cufflinks or if I should use the initial aligned BAM file.
Secondly, if it is suitable, would it make sense to before local realignment around indels using GATK prior to Cufflinks?
Thank you for your time,
cb
Similarly, I have trimmed, aligned and sorted using STAR, add read groups, and marked duplicates to my BAM file. I'm curious if this processed BAM file is suitable for input into Cufflinks or if I should use the initial aligned BAM file.
Secondly, if it is suitable, would it make sense to before local realignment around indels using GATK prior to Cufflinks?
Thank you for your time,
cb
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