Moderator: RamRS

gravatar for RamRS
RamRS18k
Reputation:
17,920
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Location:
Houston, TX
Twitter:
@_RamRS
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Google Scholar Page
Last seen:
48 minutes ago
Joined:
5 years, 3 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.

Posts by RamRS

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Answer: A: Alt allele count from 1000 genome project
... You'll need to combine a liftover operation on a 1000g VCF file (unless an hg38 version is already available) with a `bcftools annotate` operation. The `annotate` operation can copy over attributes from a reference VCF file to a target VCF file based on matching `chrom`, `pos`, `ref` and `alt`, assu ...
written 14 hours ago by RamRS18k
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Comment: C: Filter table in R based on the number of chromosomes
... "I searched" does not help, my friend. What did you search for? Did you look for "remove rows that match a condition"? And searching seldom yields the exact script you need, it only gives you pointers you can use to get to where you need to go. ...
written 15 hours ago by RamRS18k
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Comment: C: Filter table in R based on the number of chromosomes
... This should work if you have tidyverse loaded. Remember that if your aim is to *remove rows that match condition X*, you're looking to **select rows that don't match condition X**. ...
written 15 hours ago by RamRS18k
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Comment: C: Filter table in R based on the number of chromosomes
... Did you try searching online? What is the simple code you wrote? ...
written 15 hours ago by RamRS18k
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Comment: C: Filter table in R based on the number of chromosomes
... This is a pure, straightforward R question and might be closed. What have you tried? ...
written 15 hours ago by RamRS18k
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Comment: C: TypeError: 'str' object is not callable
... Did you check if you'd used `len` as a variable anywhere? ...
written 1 day ago by RamRS18k
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Comment: C: TypeError: 'str' object is not callable
... > `\r\n` will be included Could be just `\n` too, depending on the OS. You're right, the lines need to be `strip`-ped ...
written 2 days ago by RamRS18k
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Comment: C: TypeError: 'str' object is not callable
... I'd recommend avoiding keywords as variable names. For example, your code has `length = columns[3]`, which might override any function that's also called `length()`. Maybe use `xyz_length = ` ...
written 2 days ago by RamRS18k
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Comment: C: GWAS IN PLINK - SIMPLE YET COMPLICATED
... IIRC the phenotype file is just IID, FID and the phenotype column from the traditional PED format. I'm trying to find solid support for this, but while I can recall seeing it a while ago, I can't seem to find a written proof anywhere. ...
written 2 days ago by RamRS18k
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Comment: C: Faster way to get sequences from large fasta files?
... I think you can use `samtools faidx` to index the FASTA, that'll make the access faster, although I'm not sure if any tools exist that can use the faidx to speed up their operation as well as use identifiers to get the sequence. You could try `samtools faidx file.fasta; samtools faidx file.fasta ` ...
written 2 days ago by RamRS18k

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