Tophat Output Files Evaluations

Question

[narges]

Hi all,

I wanted to ask if someone knows any useful publication or website with detailed explanation about tophat output files, I mean something rather than the tophat manual itself. Thanks a lot in advance.

[Istvan Albert]

This is a good observation - we should compile posts with pointers to good review papers

[Sean Davis]

I know you are asking a general question, but is there something specific that you want to know or need to do with the files?

[narges]

Actually my next step is to run cufflinks over my dataset but I do not know before running cufflinks, what kinds of evaluating or examining for reliability of my outputs I should take into account. Ofcourse I have checked the output log files and alignment percentages mentioned in them but I do not know what is the systematic way of this transition from tophat output to packages like cufflinks.

Answer 1

[Mikael Huss]

I use RSeQC, which is pretty good IMO.

I also know of RNASeQC (yes, almost the same name) and Picard CollectRNASeqMetrics, which I have tried but for various reasons I preferred the first one I mentioned.

[Istvan Albert]

I will add this to the tools

Answer 2

[JC]

This paper was recently published, it presents QualiMap, a software to evaluate alignment data (BAM/SAM files) including RNAseq.

[narges]

Thank you so much