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Question: EAGLE-RC suitable for long-read RNA-seq? #7

Closed nadjano closed 4 months ago

nadjano commented 4 months ago

Hello,

EAGLE-RC seems like a very useful tool for Allele specific expression.

I saw the option --dp. So with this is can run EAGLE-RC on aligned long-read RNA-seq (e.g IsoSeq)? Or do you have any other recommendation of parameters for analysing long-read RNA-seq?

Thank you!

Best, Nadja

tony-kuo commented 4 months ago

Hi Nadja,

Indeed --dp is used for long RNA-seq reads, specifically those with higher base-calling error rates / indel error rates such as PacBio sequencing.

Other parameters you should be aware of are:

--gap_op [INT] Gap open penalty for use with --dp. Default is 6. For long reads that contain indel errors, 2 may be a better.

--gap_ex [INT] Gap extend penalty for use with --dp. Default is 1.

--lowmem should not be used

--rc' should not be used because it includes--lowmem`

As you're planning to use EAGLE-RC. I would perhaps suggest:

--omega=1.0e-40 --isc --mvh --verbose --dp

and optionally consider changing the gap open penalty to be lower.

Note that this will preclude you from using --ngi in eagle-rc.

Hope this helps.

nadjano commented 4 months ago

Thanks a lot for the suggestions and the quick response! That is very helpful! 😃