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?
1 answer
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:
Log in to answer this question.
-
How to Obtain Gene-Transcript Isoforms from RefSeq Format using a gff files as input?
written by mauricio.1313 •
-
Tutorial: Converting TSV file to VCF
written by barslmn •
-
Chimeric RNA (noncoding RNA) validation and quantification using RNA-seq data
written by machao9008 •
-
No enriched GO terms with 1000 more genes
written by Ruixuan •
-
SnpEff START/STOP codon not found error
written by thomasbersez
-
NCBI Accession Number to Taxonomy ID
written by mrsmith •
-
Tutorial: RepSeq data processing and analysis
written by mikhail.shugay
-
Genomic Annotation of Intervals (yes, again)
written by Tom
-
Second column in Ensembl GTF: source or biotype?
written by alex.rubinsteyn
-
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, …
written by Malachi Griffith
Is the RNA-Seq library you used stranded ?
Oh, I didn't notice it. I have to check it out. Thanks for your reply.
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)