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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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Alternative splicing signal on tandem duplicated genes #224

Open XMTian opened 1 year ago

XMTian commented 1 year ago

Hi,

Thanks for developing leafcutter!

I have a question regarding the alternative splicing signals on tandem duplicated genes.

I found a region that contains five tandem duplicated genes that show alternative splicing signals. I have checked this region among several high-quality genomes of closely related species and confirmed that this tandem gene duplication is shared in this lineage. And the similarity among these five genes in my species is from 89% to 95%. I wonder if the alt. splicing signal is a real signal or artifact that caused by the similarity among these genes.

Do you think could I trust this splicing signal? Do you have any suggestions for this phenomenon?

Thanks in advance!

Best, Xiaomeng

goldenflaw commented 1 year ago

Hi,

LeafCutter relies on accurate alignments, as such if the aligned reads are wrong then LeafCutter output will be wrong too. I would suggest you to check your read alignments.

Best, Yang

On Mon, Dec 19, 2022, 08:42 XMTian @.***> wrote:

Hi,

Thanks for developing leafcutter!

I have a question regarding the alternative splicing signals on tandem duplicated genes.

I found a region that contains five tandem duplicated genes that show alternative splicing signals. I have checked this region among several high-quality genomes of closely related species and confirmed that this tandem gene duplication is shared in this lineage. And the similarity among these five genes in my species is from 89% to 95%. I wonder if the alt. splicing signal is a real signal or artifact that caused by the similarity among these genes.

Do you think could I trust this splicing signal? Do you have any suggestions for this phenomenon?

Thanks in advance!

Best, Xiaomeng

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