Fr-Secondstrand Versus Fr-Unstranded Library Type In Tophat2

Question

[biorepine]

Dear biostars,

Does any one have experience using fr-secondstrand versus fr-unstranded library types in tophat. I am running tophat against fr-secondstrand type rna-seq reads but using default parameters (by default it is fr-unstranded ). Does it affect mapping ? thanx in advance

[Ashutosh Pandey]

It may work with the alignment of the read but you will loose information about which strand the read is coming from? The whole point of using strand specific library is that you can tell which strand your read belongs to. Read this (Tophat library type and pair orientation for illumina data)

Answer 1

[biorepine]

After checking the mapped reads carefully across known transcripts, found out that tophat some how detects the library type even though you do not specify and correctly assigns strand-specific reads. Thanx anyways if you drop by my thread.