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Forum: Illumina/Solexa 04-03-2014, 04:43 AM
Replies: 58
Views: 52,728
Posted By kmcarr
Library strandedness still matters when you are...

Library strandedness still matters when you are aligning single end reads. For Illumina TruSeq Stranded RNA libraries single end reads match the anti-sense strand of mRNA (aka reverse, firststrand of...
Forum: Illumina/Solexa 07-03-2013, 02:32 AM
Replies: 58
Views: 52,728
Posted By kmcarr
No, for this protocol you should use...

No, for this protocol you should use --stranded=yes. I was wrong.

EDIT:

Sorry, I was wrong in my original post, and dvanic was correct. If your library was prepared using the Illumina TruSeq...
Forum: Illumina/Solexa 06-05-2013, 12:30 PM
Replies: 58
Views: 52,728
Posted By kmcarr
Correct. The first cDNA strand...

Correct.



The first cDNA strand synthesized uses the actual RNA molecule as its template, so it seems a little convoluted to say "using as template the strand corresponding to the RNA molecule...
Forum: Illumina/Solexa 06-05-2013, 12:05 PM
Replies: 58
Views: 52,728
Posted By kmcarr
You're correct; sorry, brain lock on my part.

You're correct; sorry, brain lock on my part.
Forum: Illumina/Solexa 06-05-2013, 07:26 AM
Replies: 58
Views: 52,728
Posted By kmcarr
Is this true? If that is the case, then ...

Is this true?

If that is the case, then

a) the illustration above should portray the complementary strand to the RNA being used as template to synthesize (and read) the actual mRNA molecule by...
Forum: Illumina/Solexa 08-21-2012, 05:25 PM
Replies: 58
Views: 52,728
Posted By kmcarr
That is correct.

That is correct.
Forum: Illumina/Solexa 08-21-2012, 04:59 PM
Replies: 58
Views: 52,728
Posted By kmcarr
Bill, The TruSeq RNA protocol is NOT...

Bill,

The TruSeq RNA protocol is NOT directional. The appropriate --library-type option for these libraries is fr-unstranded (which is the default for TopHat).
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