Thank you very much I found the splice variant in my RNA-seq data !!!
• 0 views
•
link
written
by
mari.felix5723 •
Finding isoform in RNA-seq data
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 !
• 2,724 views
•
link
updated
by
Devon Ryan
•
written
by
mari.felix5723 •
•
written
by
mari.felix5723 •
1 answer
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.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
Isoform detection of a gene using RNAseq
written by vinishavvenugopal •
-
How represent isoforms in different tracks in a genome browser?
written by Bardt9 •
-
Hypothesis testing for isoform level TCGA RNA-seq expression data
written by deepak18 •
-
Retrieving BAM files from known isoforms
written by priscillamorris90 •
-
Question about downloading RNA-seq long reads and short reads for the same sample
written by tunl
-
Identifying isoforms de novo
written by jjrin •
-
the most frequent isoform of each gene specific to the cell line
written by ashkan
-
A way to detect nonsense mutations in RNA-Seq data
written by cpm186 •
-
cuffcompare output results
written by hana
-
Encode Genome Browser: How To Correlate Dnasei Hypersensitivity With Rna-Seq?
written by khandarius •
