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Question: how to extracts mRNA sequences with different Poly(A)tail lengths from RNA seq data
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gravatar for jaeil.han
2.1 years ago by
jaeil.han • 10
United States
jaeil.han • 10 wrote:

I am trying to compare poly(A) tail length of mRNAs in cells with different condition both at global and individual mRNA levels. However, I don't know where to start. I think I could somehow extract mRNA sequences with polyA tail from BAM file after mapping?

Can anyone give me an insight?

Thanks,
rna-seq mrna polya • 919 views
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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by jaeil.han • 10
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gravatar for Jennifer Hillman Jackson
2.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Mapping does not assemble NGS reads into consensus sequences. The tool Trinity will, producing a fasta dataset. This would allow discovery/analysis of any novel transcripts.

If you are mapping against a transcriptome, then mRNA sequences in your reference transcriptome could be captured from mapping results and then extracted into a fasta dataset. This would not capture any novel transcripts in your NGS reads.

From either, the consensus mRNA sequences could be evaluated for content, including poly-A tail length.

Hopefully this helps, Jen, Galaxy team
ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
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