Question

how to find new transcript from bam file?

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6.5 years ago

PK ▴ 130

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

next-gen alignment RNA-Seq • 2.7k views

ADD COMMENT • link updated 6.5 years ago by Federico Giorgi ▴ 740 • written 6.5 years ago by PK ▴ 130

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You can have a look to this discussion.

ADD REPLY • link 6.5 years ago by Chirag Parsania ★ 2.0k

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Read about stringtie.

ADD REPLY • link 6.5 years ago by ATpoint 85k

score 1 · Answer 1 · 2018-05-25

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6.5 years ago

Federico Giorgi ▴ 740

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

ADD COMMENT • link 6.5 years ago by Federico Giorgi ▴ 740

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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.

ADD REPLY • link 6.5 years ago by PK ▴ 130

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

ADD REPLY • link 6.5 years ago by ATpoint 85k

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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%.

ADD REPLY • link 6.5 years ago by PK ▴ 130