User: apuhegde

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apuhegde20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
3 months ago
Joined:
2 years, 3 months ago
Email:
a*******@gmail.com

Posts by apuhegde

<prev • 9 results • page 1 of 1 • next >
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COSMIC-like database for mouse sequencing data
... I have DNA sequencing data on murine samples, which I want to run through a database like COSMIC to annotate cancer-relevant mutations. I see this question has already been asked here: http://seqanswers.com/forums/showthread.php?t=70729&utm_source=feedburner&utm_medium=feed&utm_campai ...
mouse cancer cosmic mutations homologous written 4 months ago by apuhegde20 • updated 4 months ago by EagleEye4.9k
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Comment: C: SNPeff result interpretation
... Hello, this is almost 3 years late, but were you able to interpret the meaning of this finally? Please do share what you learnt, if you did. Thanks! ...
written 5 months ago by apuhegde20
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Multiple biopsy issue in MutSig and GISTIC tools
... Hi all, I need to perform GISTIC and MutSig analyses on a cohort of samples. Some of these samples have multiple biopsies taken at both A) same time point, B) different time points. I was wondering what the best way is to go about this situation for the two analyses I mentioned: Specifically: 1) ...
gistic multiple samples multiple biopsies mutsig written 5 months ago by apuhegde20
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Comment: C: Snipsift synonymous variant extraction
... Check my reply to basalganglia. ...
written 7 months ago by apuhegde20
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Comment: C: Snipsift synonymous variant extraction
... Bash uses "!" expression in its history substitution command. So it confuses your command with history substitution function and throws an error that it didn't find such a command in its history. Try temporarily turning off history substitution feature and turning it back on when you're done with y ...
written 7 months ago by apuhegde20
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Comment: C: How to do unsupervised clustering using copy number variation data?
... Could you please elaborate a little on "The key is to get a vector representation of the samples" and "they represented each tumor with a vector"? Thanks. ...
written 7 months ago by apuhegde20
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Comment: C: How to use MutSigCV correctly
... Hello, I stumbled across this thread while searching for something similar. So if I understood you correctly, after SNP annotation (I'm using Haplotype Caller), I'm left with a VCF file, from which I need to remove all the annotated SNPs. This leaves me with only un-annotated variants (which are t ...
written 9 months ago by apuhegde20
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Answer: A: how to combine RNA seq data from 4 lanes
... If I had paired-end data, I would combine all the forward read files together, and all the reverse read files together, for all lanes and all flow cells, am I right (assuming there are no batch effects due to lanes and flow cells)? One concern I have is the index (barcode) sequence for the differen ...
written 10 months ago by apuhegde20
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Update on the best pipeline for sequencing?
... It's been 6.4 years since this question was asked last: https://www.biostars.org/p/1268/ I have this same question but I see that 6.4 years ago people were of the opinion that a lot of the best practices were still under development and included quite a bit of of trial and error. I'm assuming thin ...
exome next-gen whole genome rna-seq sequencing written 16 months ago by apuhegde20 • updated 16 months ago by vchris_ngs4.3k

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