Hi folks, I am working with RNA Seq data. when i run tophat it says (Coverage-search algorithm is turned on, making this step very slow Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.) . But i don' t know why. Please explain what actually it means.
•
written
by
PK •
1 answer
The "coverage search" step is a very slow step that looks for novel splice sites (for more details, see a previous answer from here here: Coverage-search vs. no coverage-search in running Tophat ). The warning you're seeing is always printed as far as I know.
As an aside, tophat2 is very slow and no longer recommended by its authors. If this is a new project then I would use a different aligner (hisat2, STAR, etc.).
Log in to answer this question.
-
Tophat fusion error
written by baurumon •
-
Which parameters to change in Tophat default settings for homosapiens cancer data?
written by PK •
-
Am I using Tophat2 correctly? Segment-based junction search error keeps coming up.
written by aswartz85 •
-
How important is --frag-bias-correct in running Cuffdiff (it makes Cuffdiff very slow in our case)?
written by tunl
-
Coverage-search vs. no coverage-search in running Tophat
written by tunl
-
RNA seq NGS data analysis
written by poonam.bi01 •
-
Libboost error while running Tophat alignment job
written by rajesh27071992 •
-
why tophat2 saying that --max--deletion-length not recognized???
written by zizigolu
-
Tophat_Reports "Failed" Error
written by vinay kumar •
-
Coverage-Based Search In Tophat
written by jeremy
