Coverage-search algorithm is turned on, making this step very slow

Question

[PK]

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.

Answer 1

[Devon Ryan]

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.).

[PK]

Dear Ryan, Thank you for your comment. Actually i have to replicate the results that is why i am using tophat.