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Old 05-31-2013, 10:42 AM   #81
Jon_Keats
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Location: Phoenix, AZ

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Somatic Variant Calling

This is a bit of a shameless plug for one of our institutional tools developed for somatic variant calling. In our experience it is one of the best tools for paired tumor-normal/constitutional identification of somatic variants.

Check it out:
https://sites.google.com/site/seuratsomatic/

On other notes, we have been doing a decent bit of testing comparing Tophat and STAR for RNA alignments. We should be posting more in the future but here are my take aways
1) Using updated genomes and GTF dramatically improves the TOPHAT alignment rates (we moved to the new 1000G reference hs37d5 from the inital version and from ensembl 64 to ensembl 70)
2) STAR is smoking fast
3) STAR does a much better job of aligning indels, particularly large indels (this might be a tophat settings issue, it doesn't seem that we really leverage the bowtie2 gapped alignments in tophat... I could be wrong)
4) Expression estimates of same samples aligned with STAR or TOPHAT are nearly identical (r2>0.97)
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Old 05-31-2013, 11:07 AM   #82
GenoMax
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Quote:
Originally Posted by Jon_Keats View Post
Somatic Variant Calling

This is a bit of a shameless plug for one of our institutional tools developed for somatic variant calling. In our experience it is one of the best tools for paired tumor-normal/constitutional identification of somatic variants.

Check it out:
https://sites.google.com/site/seuratsomatic/

On other notes, we have been doing a decent bit of testing comparing Tophat and STAR for RNA alignments. We should be posting more in the future but here are my take aways
1) Using updated genomes and GTF dramatically improves the TOPHAT alignment rates (we moved to the new 1000G reference hs37d5 from the inital version and from ensembl 64 to ensembl 70)
2) STAR is smoking fast
3) STAR does a much better job of aligning indels, particularly large indels (this might be a tophat settings issue, it doesn't seem that we really leverage the bowtie2 gapped alignments in tophat... I could be wrong)
4) Expression estimates of same samples aligned with STAR or TOPHAT are nearly identical (r2>0.97)
Create a separate post too otherwise it may not be noticed by people who are looking for a tool like this. Someone had a recent post with just this question.
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Old 11-25-2014, 10:09 PM   #83
Jon_Keats
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Its been a very long time since I've updated this thread. I've recently added a couple of new MAC computers that I use for development and tertiary analysis. And I wanted an updated build protocol to install all the different applications we have outlined in earlier versions of this thread. If you want to see the updated build instructions they are available on my lab website (http://www.keatslab.org/computation/...ure-a-machine1)
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Old 08-26-2015, 04:16 PM   #84
Jon_Keats
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For those people following this thread.

We are recruiting Post-Doctoral Fellows for one of our large cancer genomics programs. If you are interested in working in a cutting edge research institute focused on translational genomics and leading a major project please send a cover letter and CV to Dr Keats. (www.keatslab.org)(www.tgen.org)
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