Question: From bam files to isoform read counts
0
gravatar for ddzhangzz
3.0 years ago by
ddzhangzz90
United States
ddzhangzz90 wrote:

I downloaded RNASeq bam files from TCGA data portal. I am interested in the expression analysis at isofrom level and wondering how to translate these bam files into counts at each isoform. I have done some analysis at gene level using star or htseq-count but fresh to isoform analysis. Could somebody have me some suggestions. I knew there are softwares such as rMATs for alternative splicing (AS) analysis but what I wanted are the counts for each isoform rather than the AS analysis.

rna-seq • 1.2k views
ADD COMMENTlink modified 2.6 years ago by firatuyulur300 • written 3.0 years ago by ddzhangzz90

You would want to carefully check how multi-mappers were handled if you are starting with BAM files and considering isoforms.

ADD REPLYlink written 3.0 years ago by genomax80k
0
gravatar for Benn
3.0 years ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

There is an example (case study) in the edgeR user's guide. Chapter 4.5. They use featureCounts first instead of htseq.

https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

ADD COMMENTlink written 3.0 years ago by Benn7.9k
0
gravatar for firatuyulur
2.6 years ago by
firatuyulur300
firatuyulur300 wrote:

Try sailfish They are not the exact counts but would work for many purposes.

ADD COMMENTlink written 2.6 years ago by firatuyulur300
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