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Question: Tophat library type options
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gravatar for Mo Heydarian
2.8 years ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hi All,

I am working with single end RNAseq data and noticed recently that using the different 'library type' (strandedness) options for alignment with Tophat in Galaxy all result in the same alignments. Whether I use 'fr unstranded', 'fr first strand', or 'fr second strand' as the 'library type', the aligned reads for all three settings consistently map to the same strand. 

Splice junctions seem to be handled differently (and appropriately) with the different 'library type' options. 

I've obtained the same results on Galaxy Main and Galaxy Cloudman. 

Insight would be appreciated and I am happy to share an example history. 

 

Thanks in advance!
single-end stranded tophat rnaseq • 1.2k views
ADD COMMENT • link •
modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by Mo Heydarian ♦ 830
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello Mo,

Please see the how library type is used by the tool here in the manual (Options: Library Type): http://ccb.jhu.edu/software/tophat/manual.shtml

The strand the read aligns to (if the match is strong/spliced) would not change, but you may get fewer hits if the actual library type differs from the one selected. The two latter choices consider sequencing direction of the read differently when determining the alignments to retain, to consider as proper pairs, etc.

The google group for the tool might be a good place to review prior Q&A about library type choices and results. A link to that is at the same web site as the manual above.

Others are welcome to add more details from their experience.

If there are no changes in the output at all and you think this might be a tool bug, send in some shared histories and we can dig deeper. galaxy-bugs@lists.galaxyproject.org. 

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks, Jen. I'll send an example in a shared history to galaxy-bugs@lists.galaxyproject.org. 

ADD REPLY • link written 2.8 years ago by Mo Heydarian ♦ 830
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