Question: From bam files to isoform read counts
0
gravatar for ddzhangzz
2.1 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 • 904 views
ADD COMMENTlink modified 21 months ago by firatuyulur280 • written 2.1 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 2.1 years ago by genomax67k
0
gravatar for Benn
2.1 years ago by
Benn6.8k
Netherlands
Benn6.8k 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 2.1 years ago by Benn6.8k
0
gravatar for firatuyulur
21 months ago by
firatuyulur280
firatuyulur280 wrote:

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

ADD COMMENTlink written 21 months ago by firatuyulur280
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1514 users visited in the last hour