Question: Removing artifact from evolved tuxedo pipeline
gravatar for pablo_iturralde
17 months ago by
pablo_iturralde0 wrote:


I've processed a data set that had ribosomal RNA contamination through the evolved tuxedo pipeline (see picture below) after removing rRNA using bbduk from bbmap: [Pipeline for Ribbosomal RNA contaminated reads][1]Screen-Shot-2019-04-10-at-10-57-30-AM

Once I started visualizing volcano plots I noticed some strange artifacts that I haven't been able to put my finger on.

[Volcano plot, arrows point clusters][2] Screen-Shot-2019-04-10-at-10-54-56-AM

It appears there are several transcripts that are clustering in certain areas of the volcano plots. My first thought was they were NANs and needed removal after means were calculated after ballgown object was created using !=NAN approach.

That did not change the clustering on the volcano plot though, I thought maybe removing exons that = 0 on the string tie output ( CTAB files) may do it but its a bit tricky as all 5 ctab files need equal editing from what I read ?

Any insight is appreciated.

Best, Pablo

rna-seq • 378 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by pablo_iturralde0

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

ADD REPLYlink written 17 months ago by RamRS30k
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