User: cacampbell

gravatar for cacampbell
cacampbell40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 years, 1 month ago
Joined:
4 years, 5 months ago
Email:
c*********@ucdavis.edu

Posts by cacampbell

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Split SAM file into smaller SAM files by line count
... YEP... I definitely did use echo instead of cat. Oops. ...
written 3.3 years ago by cacampbell40
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Comment: C: Split SAM file into smaller SAM files by line count
... Thanks, this does the trick -- I think my problem was that I stupidly used "echo" instead of "cat" -- so of course the file was invalid. ...
written 3.3 years ago by cacampbell40
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Split SAM file into smaller SAM files by line count
... So, I am trying to split a SAM file into many smaller SAM files -- by line number, where the line number is a multiple of 8. I tried the following series of commands: samtools view -H Mapped_Pila/LBG07/LBG07_pe.sam > Mapped_Pila/LBG07/LBG07_pe.header.sam && samtools view Mapped_Pil ...
sam written 3.3 years ago by cacampbell40 • updated 3.3 years ago by george.ry1.1k
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Answer: A: BBTools - Repair.sh bug (?)
... Java version error due to nodes not finding modulepath -- see comments ...
written 3.4 years ago by cacampbell40
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Comment: C: BBTools - Repair.sh bug (?)
... Hi Brian, I believe that the java problem was the issue. We do use an environment module system, and I was loading java 1.8 for each of these jobs. Nonetheless, it appears that three nodes are unable to find the modulepath and thus default to java 1.6. I have notified our system administrators. I ...
written 3.4 years ago by cacampbell40
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BBTools - Repair.sh bug (?)
... Hello https://www.biostars.org/u/14684/, I get an ambiguous stack trace in 1/8 - 1/10 of repair.sh jobs (but not other tools), and I cannot seem to reliably reproduce the problem. Running the same jobs again on the same files only produces errors in the same files by rare coincidence, if at all. ...
bbtools written 3.4 years ago by cacampbell40
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Comment: C: BBMap: Mapping Fails
... Okay, Will do thanks. I will reformat to phred+33, and try again. This seems like it should solve the issues I am having with this data. ...
written 3.6 years ago by cacampbell40
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Comment: C: BBMap: Mapping Fails
... Yes, Illumina format data phred+64, according to the Report provided with the data. So, that's weird right? ...
written 3.6 years ago by cacampbell40
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Comment: C: BBMap: Mapping Fails
... Hi Brian, After leaving this project for a few weeks and coming back to it, I ran BBDuk2 again -- using quality of 10 to trim, and discovered that 99.9% of bases were being trimmed. Would looking at the fastqc information verify this result? If this isn't some kind of bug, is... is this bad? Is t ...
written 3.6 years ago by cacampbell40
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Comment: C: BBMap: Mapping Fails
... So, I was on vacation last week, but back at it today. Things are even less clear at this point, as it turns out that BBDuk had output empty files with a similar error to the ones here. So, I am going to be trying reformat.sh on the original files. If that works, then I will continue through the s ...
written 3.7 years ago by cacampbell40

Latest awards to cacampbell

Popular Question 3.3 years ago, created a question with more than 1,000 views. For RNA-SEQ DEG -- No Control
Scholar 3.4 years ago, created an answer that has been accepted. For A: FunPat Differential Testing Plot Error
Scholar 4.4 years ago, created an answer that has been accepted. For A: FunPat Differential Testing Plot Error

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