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djhn75 / RNAEditor

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Why BWA and not spliced mapper? #5

Closed solyris closed 6 years ago

solyris commented 7 years ago

Hi, I am just wondering why BWA is picked as the aligner in this package and not a spliced aware aligner like STAR or Tophat?

djhn75 commented 7 years ago

Hi, we are currently working to integrate star into the pipeline. But in the current pipeline it is ok to use a non splice aware mapper, because we do a local realignment afterwards, this diminishes splicing errors.

David

Am 08.03.2017 um 08:16 schrieb solyris:

Hi, I am just wondering why BWA is picked as the aligner in this package and not a spliced aware aligner like STAR or Tophat?

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-- David John Institute of Cardiovascular Regeneration Theodor-Stern-Kai 7 D-60590 Frankfurt am Main +49 69 6301 87952 John@med.uni-frankfurt.de

solyris commented 7 years ago

Hi David,

Thanks for the prompt reply. I have some problems with RNAEditor use with regards to the BWA in the pipeline. In particular I think the BWA used in your package is made to handle only reads length of 30-45bp only and for my project which is RNA-seq of length 100bp, the mapping efficiency is abysmal at only 1% mappable reads. I have mapped this set of data with STAR in a prior exercise and gotten over 90% mappable reads. This issue I think is caused by the BWA aln mode used in your pipeline which the later BWA supports longer reads with the BWA mem mode instead. I hope you can consider updating the pipeline to support long reads too instead of the short reads only.

I am trying to work around this as well by changing the MapFastq.py file, may I know if that is the correct direction to take? Any advise on other files which needs updating is highly appreciated as well.

djhn75 commented 7 years ago

Dear Solyris, yes the MapFastq.py is the correct file to chnage the mapper. You have to adfjust line number 85,90,95 for paire-end and 100,106 for single-end. But please make sure to integrate the following read Groups "@RG\tID:bwa\tSM:A\tPL:ILLUMINA\tPU:HiSEQ2000"

If you suceed please let me know, then i would be happy to integrate it as a new branch.