Moderator: Ram

gravatar for Ram
Ram15k
Reputation:
15,110
Status:
Trusted
Location:
New York
Twitter:
@_RamRS
Scholar ID:
Google Scholar Page
Last seen:
2 minutes ago
Joined:
4 years, 11 months ago
Email:
r****@nyu.edu

Bioinformatician turned Microsoft technologies developer turned bioinformatician. I love messing with text. UNIX>R>Python>Perl programmer, Excel pro, master Googler, database expert. 

I'm an amateur biologist interested in translational human genetics and healthcare.

Twitter: @_ramrs

Posts by Ram

<prev • 3,256 results • page 1 of 326 • next >
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Comment: C: Samtools mpileup returns empty vcf file
... That is strange. Maybe check out the bams.list to ensure line endings are fine and the BAM files exist at the right locations? ...
written 1 day ago by Ram15k
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Answer: C: Samtools mpileup returns empty vcf file
... From a first glance, I can see that the `bcftools` command is not proper. When input is stdin (being piped in from a previous command), you need the stdin indicator `-` as specified in the specs: >BCFtools is designed to work on a stream. It regards an input file "-" as the standard input (stdin ...
written 1 day ago by Ram15k
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Comment: C: selecting the templates for homology modelling from modeller
... Please do not add answers unless you're answering the top level question. This belongs as a reply to my comment. Please see http://biostars.org/t/how-to posts to learn how to use the forum better. I've moved your post to a comment for now. ...
written 2 days ago by Ram15k
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Comment: C: Extracting allele, Genotype from VCF file
... Let's not continue with this discussion any longer please, it is not relevant to the topic on hand. ...
written 2 days ago by Ram15k
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Comment: C: reasons for htseq-count with zero features
... I think auto-correct changes a bunch of `fine`s to `find`s. Can you edit your post and correct those please? ...
written 2 days ago by Ram15k
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Comment: C: Converting UUID downloaded from GDC to TCGA names
... I guess you can either do the R->py algorithm conversion yourself, or branch out to R as an intermediate step. I don't think it's fair to expect a solution in your language of choice without good reason why an existing solution is not usable. ...
written 2 days ago by Ram15k
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Comment: C: selecting the templates for homology modelling from modeller
... It's been years since I used modeller but isn't the basic premise that you don't work with a template that's at ~40%? You need around 60-70% for template based alignment to work well, no? Have you looked to see what negative e-values could mean? If they're all in a narrow range and not too negative ...
written 2 days ago by Ram15k
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Comment: C: Extracting allele, Genotype from VCF file
... I think there is a misunderstanding - I did not imply who said something first. I merely pointed to the fact that the answer as it existed then should have been a comment like `` was. ...
written 2 days ago by Ram15k
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Comment: C: Extracting allele, Genotype from VCF file
... I think this should be a comment, as it's more of a suggestion than a solution. See, for example, cpad's comment pointing to the same resource. ...
written 3 days ago by Ram15k
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Comment: C: Extracting allele, Genotype from VCF file
... Doesn't look like vcfR does streaming read, so I would not recommend it as it's not a great idea to build an in-memory object of an entire VCF file. A better strategy would be to use closer-to-bare-metal tools such as bcftools to extract information, then use R or Python to compute on extracted info ...
written 3 days ago by Ram15k

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Scholar 6 weeks ago, created an answer that has been accepted. For C: variant calling for more than 60 samples using haplotype caller
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