Dear RNA-seq community,
I have run Tuxedo (and data looks good in cummeRbund) but I am wondering if should have done it slightly differently.
Reading more carefully the protocol I am now wondering if I should have incorporated the argument "--library-type" in my tophat2 script. The protocol encourages users with well annotated genome (pag 567) to run the alternate protocol ‘Quantification of reference annotation only’ (I used the Arabidopsis genome, strand specific sequencing).
So my questions is, should I run the analysis again? If so, will the output using this new argument ("--library-type" ) be the same as the output without it (in other words, will i still see the "accepted_hits.bam" to proceed with the cufflinks?).
Please let me know what you think.
Many thanks in advance,
-G
Tuxedo Protocol: Nature Protocols 7, 562–578 (2012) doi:10.1038/nprot.2012.016
I have run Tuxedo (and data looks good in cummeRbund) but I am wondering if should have done it slightly differently.
Reading more carefully the protocol I am now wondering if I should have incorporated the argument "--library-type" in my tophat2 script. The protocol encourages users with well annotated genome (pag 567) to run the alternate protocol ‘Quantification of reference annotation only’ (I used the Arabidopsis genome, strand specific sequencing).
So my questions is, should I run the analysis again? If so, will the output using this new argument ("--library-type" ) be the same as the output without it (in other words, will i still see the "accepted_hits.bam" to proceed with the cufflinks?).
Please let me know what you think.
Many thanks in advance,
-G
Tuxedo Protocol: Nature Protocols 7, 562–578 (2012) doi:10.1038/nprot.2012.016