RNA Seq

Question

[shrinka.genetics]

Hello Anybody could you please let me know

1) Which one is most suitable package for Isoform quantification

2) What should be the form of input data? FASTQ, bam etc?

Shrinka

[jared.andrews07]

Please use more descriptive post titles in the future - "RNA Seq" doesn't really describe your question well at all. They will help your questions get answered more quickly and make them easier to find for others with similar questions.

Answer 1

[jared.andrews07]

There are many ways to quantitate transcripts. Some work off aligned BAMs (e.g. RSEM), other pseudoalignment methods can go directly from FASTQs (e.g. Salmon). Salmon is very easy to use, very fast, and highly accurate (and can also work on aligned BAMs if you want to go that route). You'd likely be well-served by reading the salmon papers/docs. The DESeq2 vignette is also a classic "must read" for typical differential gene analysis. There's also a Bioconductor workflow built on the DRIMSeq and DEXSeq packages that walks through a differential transcript usage (DTU) analysis if you've got a need for that.

[swbarnes2]

Though I think DESeq is not suitable for finding differential transcript expression, just differential gene expression.

[jared.andrews07]

Yes, that is correct. The other workflow I posted is a good Bioc-based alternative to DESeq2. It wasn't really clear where the OP wanted to go after quantifying.