How to determine the strand of a transcript?

Question

[Michael Chen]

I got some transcript annotation from cuffnorm. However, it seemed that there was no strand information in transcript annotation. I tried some transcript id, e.g. NR_132124, on NCBI database; the database show the direction of the specific transcript. It seemed that we can determine the strand of a transcript, but no turn-key solution. Any suggestion?

[Update]

I had accession id, e.g. NR_000016, its gene id, e,g. SNORD36C, and genome coordinate, e.g. chr9:136215068-136218280, but no strand info. Can I get strand by the above info?

[Nicolas Rosewick]

Is the RNA-Seq library you used stranded ?

[Michael Chen]

Oh, I didn't notice it. I have to check it out. Thanks for your reply.

[Nicolas Rosewick]

Yes first thing to know if it's stranded and also which preparation type (polyA enriched or rRNA depleted). Also the read length is important to know in order to tune the parameters (even if default ones are ok)

Answer 1

[Istvan Albert]

The library preparation will determine the method that will need to be used. A description of what you are up against is here:

http://salmon.readthedocs.io/en/latest/salmon.html#what-s-this-libtype

Other related questions:

• Strand specific pair end Illumina sequencing
• How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand