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Alternative Splice Reads

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

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updated by waqaskhokhar999 waqaskhokhar999 • written by Varun Gupta Varun Gupta

2 answers

There are several tools that report split-reads:

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

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updated by Ram Ram • written by David Langenberger David Langenberger

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

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written by waqaskhokhar999 waqaskhokhar999

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