cmartinezruiz
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Activity overview
Latest activity by cmartinezruiz-
cmartinezruiz commented,
Thank you very much for the explanation David Benjamin, it is very informative. The library preparation we used for RNAseq is stranded. This means that each strand is amplified separately during th...
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cmartinezruiz commented,
I still get the false negative orientation, even when using "-read-filter NotSupplementaryAlignmentReadFilter". So I think I will just skip the orientation bias model as you suggest. I have uploade...
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cmartinezruiz commented,
Ah yes, sorry I should have mentioned that. I did add the LearnReadOrientationModel to the pipeline, although given the false negatives I am getting I was considering skipping that step.
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cmartinezruiz commented,
David Benjamin Unfortunately I am not a specialist in using RNA for detecting variants either. I have been testing it on some of the samples I am running. By adding the filter "-read-filter NotSupp...
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cmartinezruiz commented,
Yes, of course! No worries
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cmartinezruiz commented,
David Benjamin I also noticed that a very large proportion of false negatives were flagged as "orientation". I checked by looking at mutations that we know are expressed and that therefore should ...
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cmartinezruiz commented,
Hello David Benjamin Bhanu Gandham, Has there been any progress on this front by any chance? I did manage a way around which consist in restricting the variant call exclusively to exons and removin...
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cmartinezruiz commented,
Hello David Benjamin and Bhanu Gandham, I have uploaded a file to the ftp server called 'to_gatk_rna_mtect2_artefact.zip' This zip file contains the following documents: gatk_subsample_focal_1000bp...
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cmartinezruiz commented,
Here are a couple screen shots of the RNAseq bam used (top track) and the out.bam file for that region. The SNV in the screenshot is the first of the list of 10 SNVs I sent in my earlier message ...
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cmartinezruiz commented,
Sorry, here are the contents of the stats file: #<METADATA>Ln prior of deletion of length 10=-16.668707731660547#<METADATA>Ln prior of deletion of length 9=-16.668707731660547#<METADATA>Ln prior of...