Question: how to find new transcript from bam file?
1
gravatar for barrypraveen
4 weeks ago by
barrypraveen10
barrypraveen10 wrote:

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

rna-seq alignment next-gen • 188 views
ADD COMMENTlink modified 4 weeks ago by Federico Giorgi390 • written 4 weeks ago by barrypraveen10
1

You can have a look to this discussion.

ADD REPLYlink written 4 weeks ago by Chirag Parsania890

Read about stringtie.

ADD REPLYlink written 4 weeks ago by ATpoint4.4k
1
gravatar for Federico Giorgi
4 weeks ago by
Columbia University
Federico Giorgi390 wrote:

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 COMMENTlink modified 4 weeks ago • written 4 weeks ago by Federico Giorgi390

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 REPLYlink written 4 weeks ago by barrypraveen10

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

ADD REPLYlink written 4 weeks ago by ATpoint4.4k

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 REPLYlink written 4 weeks ago by barrypraveen10
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