Question

Finding isoform in RNA-seq data

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6.5 years ago

mari.felix5723 ▴ 10

Hello everyone,

I'm trying to find how to look for a particular isoform in RNA-seq data. In fact I'm interested in a protein that has two isoforms.

I am wondering if one of the isoform in particular is translated in mRNA in human ES cells.

How can I look for that ? I'm new to the RNA-seq analysis and I'm not sure how to proceed... I found RNA-Seq BAM data for hES but I don't know what to do from there.

Any advice would be greatly appreciated !

RNA-Seq isoform splice variant human ES • 2.0k views

ADD COMMENT • link updated 6.5 years ago by Devon Ryan 104k • written 6.5 years ago by mari.felix5723 ▴ 10

score 1 · Answer 1 · 2017-11-01

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6.5 years ago

Devon Ryan 104k

If you already have a BAM file, then the simplest thing to do would be to load that in IGV and have a look at your gene of interest. IGV can make sashimi plots too, so you can also use that to eye ball which isoform(s) is/are actually being expressed.

ADD COMMENT • link 6.5 years ago by Devon Ryan 104k

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Thank you very much I found the splice variant in my RNA-seq data !!!

ADD REPLY • link 6.5 years ago by mari.felix5723 ▴ 10

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Is there a better way than using IGV to draw sashimi plots or any similar plot for exon/junction coverage that can output a publication quality image ?

ADD REPLY • link 6.1 years ago by khhgng ▴ 70