how to find new transcript from bam file?
1
1
Entering edit mode
6.0 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 • 2.5k views
ADD COMMENT
1
Entering edit mode

You can have a look to this discussion.

ADD REPLY
0
Entering edit mode

Read about stringtie.

ADD REPLY
1
Entering edit mode
6.0 years ago

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
0
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

Login before adding your answer.

Traffic: 1805 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6