Alternative Splice Reads

Question

[Varun Gupta]

Hi I have a question.I am working on RNA-seq data. I am interested in finding the splice reads. How do we identify alternative splice reads from a SAM file.

Hope to hear soon

Regards

Answer 1

[David Langenberger]

There are several tools that report split-reads:

• segemehl
• Tophat
• SpliceMap
• MapSplice
• SoapSplice
• and many many more....

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You just map your reads using one of these tools and they will report you the splice junctions.

Important: Some of them need paired-end reads

Answer 2

[waqaskhokhar999]

These work well for when we map on a genomic reference.... what if we need to map on a transcriptomic reference?