From bam files to isoform read counts

Question

[ddzhangzz]

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.

[GenoMax]

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

Answer 1

[Benn]

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

Answer 2

[firatuyulur]

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