User: flyamer

gravatar for flyamer
flyamer30
Reputation:
30
Status:
New User
Location:
Russian Federation
Last seen:
4 months ago
Joined:
3 years, 6 months ago
Email:
f******@gmail.com

about me

Posts by flyamer

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Checking fastq is valid
... Yes, it raises an error if sequence and quality strings have different length. ...
written 4 months ago by flyamer30
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Comment: C: Checking fastq is valid
... Ha, I don't know why not, good idea, thanks! I checked, seems like it at least picks up differences in sequence and quality lengths. ...
written 4 months ago by flyamer30
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Checking fastq is valid
... Hi, I have a suspicion one or more of my fastq files is corrupted: some reads have sequence and quality of different lengths, for example. Would this python script work to detect a problem? import sys from Bio import SeqIO for record in SeqIO.parse(sys.stdin, "fastq"): pass And ...
next-gen sequencing written 4 months ago by flyamer30 • updated 4 months ago by apa@stowers320
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Comment: C: Splitting fastq from stdin into multiple files ?
... Thanks for the idea! But can it split the file and not only give N reads? ...
written 13 months ago by flyamer30
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Comment: C: Splitting fastq from stdin into multiple files ?
... Thanks! That's interesting! ...
written 13 months ago by flyamer30
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Comment: C: Splitting fastq from stdin into multiple files ?
... Can you please provide an example? I am not very familiar with bash unfortunately. ...
written 13 months ago by flyamer30
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Comment: C: Splitting fastq from stdin into multiple files ?
... My guess is it will be smaller, and you are probably right that I should just forget this. But except for the benefit of splitting on-the-fly, I am really surprised this is not working as it should and would like to understand why... ...
written 13 months ago by flyamer30
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Comment: C: Splitting fastq from stdin into multiple files ?
... Thanks, I know about this, but I want to start mapping while I'm still splitting the file. Maybe it's too much to ask of course... ...
written 13 months ago by flyamer30
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Splitting fastq from stdin into multiple files ?
... Hi, I am trying to split a fastq stream using a python script into files with defined number of reads and immediately start a mapping job on newly created files. All this is happening on an SGE cluster, that's why I want to map reads in small chunks in parallel. The problem I encounter is that start ...
python fastq written 13 months ago by flyamer30 • updated 13 months ago by Jorge Amigo9.6k
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Comment: C: Get bedgraph file from CEL affymetrix file
... Thank you, I've seen it already though. Unfortunately it requires Affy Tiling Array software which only works under Windows as far as I can tell. ...
written 2.0 years ago by flyamer30

Latest awards to flyamer

Scholar 4 months ago, created an answer that has been accepted. For A: Checking fastq is valid
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bedtools intersect - something wrong with chromosome numbers >= 10?

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