User: Weronika

gravatar for Weronika
Weronika300
Reputation:
300
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Location:
Stanford
Last seen:
6 years, 2 months ago
Joined:
8 years, 2 months ago
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Posts by Weronika

<prev • 45 results • page 1 of 5 • next >
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Answer: A: Looking For Linux Vendors To Order A Centos/Ubuntu Based Webserver To Host Bioin
... I know this is an old question, but for the benefit of people who find it years later like I did - ZaReason is a small company that sells Linux desktops/laptops/servers, and I've had good experiences with them (I got a desktop to be used as a small data analysis server at work, and a high-end laptop ...
written 6.8 years ago by Weronika300
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Answer: A: Trim Reads In Bz2 Fastq Files
... Looks to me like you're basically doing it right - you have to use bzcat and then gzip to convert from .bz2 to .gz files, and since bowtie takes .gz files, that seems to be the best way to go. Doing it in parallel on multiple files (see the other answer/comments) sounds like a good idea. In genera ...
written 7.1 years ago by Weronika300
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Comment: C: How To Output Postscript Using Dnaplotter?
... Huh, that is weird! I have no idea why it'd do that. ...
written 7.1 years ago by Weronika300
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Comment: C: How To Output Postscript Using Dnaplotter?
... Ah, I see. Glad you got it working! Getting a print service installed on Linux might not be that hard either. I have http://en.wikipedia.org/wiki/CUPS, it works great and has a print-to-file option without me needing to install any virtual printer as far as I remember. ...
written 7.1 years ago by Weronika300
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Comment: C: How To Output Postscript Using Dnaplotter?
... Huh? What do you mean "the print function can't work" - what happens when you try it? I'm on Linux too (Ubuntu 10.04), and it worked for me... Just do File->Print from the menu and check the "Print to File" box. Although I was using the Java Web Start version rather than the standalone download ...
written 7.1 years ago by Weronika300
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Answer: A: How To Output Postscript Using Dnaplotter?
... I can't find any direct save-as-Postscript method in the current version (just downloaded it and ran it), but you can just do File->Print and then print to file as Postscript or pdf. Or does that not work for you? ...
written 7.1 years ago by Weronika300
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Comment: C: What Does This Error From Cvtree Mean?
... Well, it says "check your file type", so you should do that, and make sure they're in fact plain text files. What do you get when you run file YOUR_FILENAME in the terminal? What does it look like if you try to open the input file in a very basic text editor (less or gedit or Notepad or something)? ...
written 7.1 years ago by Weronika300
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Answer: A: Parsing A Fasta File By Columns
... Or if you wanted to avoid having all the sequences in memory at once (if your file is very large) - another python option that processes the file sequence by sequence and adds up the base frequencies: from Bio import SeqIO # first just get the first sequence, and set up a list of base:count dictio ...
written 7.2 years ago by Weronika300
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Comment: C: Sequencing And Strands
... There is no contradiction between saying that there is a convention and that the conventional designation is arbitrary. ...
written 7.2 years ago by Weronika300
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Answer: A: Comparing Quality Of Read 1 And Read2 Of Illumina Pe
... I usually use FASTX_Toolkit to get the per-base quality box-whisker plot (and a nucleotide distribution plot). I'm not aware of any tool or standard method specifically for comparing qualities between two datasets, but unless your needs are very specific, I'd probably stick with something similar t ...
written 7.2 years ago by Weronika300

Latest awards to Weronika

Supporter 6.2 years ago, voted at least 25 times.
Voter 6.2 years ago, voted more than 100 times.
Commentator 7.1 years ago, created a comment with at least 3 up-votes. For C: How To Output Postscript Using Dnaplotter?
Student 8.2 years ago, asked a question with at least 3 up-votes. For Programming The Beckman Coulter Biomek Fx Robot
Popular Question 8.2 years ago, created a question with more than 1,000 views. For Programming The Beckman Coulter Biomek Fx Robot
Popular Question 8.2 years ago, created a question with more than 1,000 views. For How Many Pass-Filter Reads Should I Expect From An Illumina Gaii Run?
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Removing Adaptors From .Fasta And .Qual Files
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: How To Best Deal With Adapter Contamination (Illumina)?

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