how to find new transcript from bam file?

Question

[PK]

Hi, I have many BAM and BED files. I am looking some novel transcripts (missed) from my BAM file. Is there any way to extract new transcripts from my BAM file. any suggestion

[Chirag Parsania]

You can have a look to this discussion.

[ATpoint]

Read about stringtie.

Answer 1

[Federico Giorgi]

Cufflinks used to be the most popular, but I would suggest StringTie (also from Johns Hopkins University), because it is more accurate for intronic and intron-retaining transcripts. They both require a BAM file as input and an optional transcript track annotation file (GFF3 or GTF)

Cufflinks

StringTie

[PK]

Thanks for your suggestion. The problem is i try to find smallRNA and I already tried with cufflinks but not satisfied. I can try stringtie.

[ATpoint]

Do you try to get smallRNAs from standard RNA-seq or from smallRNA-seq?

[PK]

it's very hard to say because we prepared the samples in a different way. it reduces the rRNAs from 80% to 20% and my snoRNAs are enriched from 5% to 30%.