Another way to identify of the library type your data

Question

[arronar]

Hi.

If you don't know the library type of your sequenced data to use with tophat, tophat's manual says :

One possible way to figure out the correct library-type is to run TopHat with a small subset of the reads (e.g., 1M) as follows.

1. run TopHat with fr-firststrand and count the number of junctions in junctions.bed (one of the output files from TopHat)
2. run TopHat with fr-secondstrand and count the number of junctions in junctions.bed

Since the splice junction finding algorithm of TopHat makes use of library-type information (if provided), one of the two TopHat runs would result in many more splice junctions than the other one. You can then use the library type that gives more junctions. If this is not the case TopHat might not work well with your sequencing protocol. Please let us know more details about your protocol so we can add support for new library types.

Is there any other way to answer that question?

Answer 1

[Ashutosh Pandey]

Another tool: http://rseqc.sourceforge.net/#infer-experiment-py

For non stranded libraries, the strandedness of reads (if they align to the forward or the reverse strand of the reference fasta) and the strandedness of transcripts (determined from their gtf annotation file) should be independent.

[arronar]

Thank you very much. Now. I will compare those results with the way of the tophat manual where both runs returned me "JUNC0000106"