RNA Seq
1
0
Entering edit mode
3.6 years ago

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

Isoform Quantification • 1.2k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
2
Entering edit mode
3.6 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2603 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6