Moderator: Michael Dondrup
Michael Dondrup ♦ 45k
- Reputation:
- 45,270
- Status:
- Trusted
- Location:
- Bergen, Norway
- Website:
- https://licebase.org/
- Last seen:
- 40 minutes ago
- Joined:
- 8 years, 11 months ago
- Email:
- m*******@gmail.com
PhD in bioinformatics. Currently Researcher at the Sea Lice Research Centre, responsible for LiceBase, an infrastructure for genomic resources of sea lice, and analysis of genomics data from emerging genomes.
Posts by Michael Dondrup
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Comment:
C: loop several conditions R
... Not sure if that question really fits here, but for now your code is faulty:
ngenes<-nrow(PGC_predix_1)
PGC_predix_1 is undefined, or possibly defined elsewhere in your environment, maybe PGC_predix was meant.
That is why you get the same output, the number of rows in this variable.
It pr ...
written 3 days ago by
Michael Dondrup ♦ 45k
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Comment:
C: Imagining Alien Biology
... Hi, there's a SE site for this: https://worldbuilding.stackexchange.com/ you could try there with a bit more concrete question. ...
written 3 days ago by
Michael Dondrup ♦ 45k
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... Applications are invited for a 3 year position as Postdoctoral Fellow in
the Computational Biology and Gene Regulation Group at the Norwegian
Centre for Molecular Medicine, University of Oslo, a Nordic EMBL partner
for Molecular Medicine. The research group is lead by Anthony Mathelier
(http://m ...
written 17 days ago by
Michael Dondrup ♦ 45k
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... Might be, or it could cause a consequential error. Please post the script as a text file (for easy copy paste for us to test). 141 is a SIGPIPE and I guess you have a superfluous pipe character in your call. ...
written 19 days ago by
Michael Dondrup ♦ 45k
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... Hi, I agree that it would be better to post your script as text. Anyway, you seem to use environment modules from http://modules.sourceforge.net/ I haven't seen this done before for bioinformatics tools, but there might be a good reason to do it that way in your case, it is worth finding out the mot ...
written 19 days ago by
Michael Dondrup ♦ 45k
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Comment:
C: Strange Error while running STAR.
... This might be related to your zcat options, they look funny, in particular zcat doesn't have -c switch, -c is used with gunzip to cause equal behavior as zcat.
Try:
--readFilesCommand "zcat"
or
--readFilesCommand "zcat -f"
or
--readFilesCommand "zcat -f --stdout"
...
written 4 weeks ago by
Michael Dondrup ♦ 45k
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Comment:
C: Four protein structures
... Hello hisham.alhawal!
We believe that this post does not fit the main topic of this site.
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to ...
written 5 weeks ago by
Michael Dondrup ♦ 45k
• updated
5 weeks ago by
zx8754 ♦ 6.2k
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... Neither am I, sorry, but maybe you can download an older version of bwa that supports colorspace. ...
written 5 weeks ago by
Michael Dondrup ♦ 45k
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... Oh, these could be colorspace data, they need to be analysed differently! Try option -c with bwa and see if that improves the alignment. See http://seqanswers.com/forums/showthread.php?t=16621 ...
written 5 weeks ago by
Michael Dondrup ♦ 45k
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... It is rare for current RNA-seq protocols to see failed sequence quality and N content. Check how the fastq extraction went well, just download and extract again using SRA toolkit. Then possibly you need to apply quality trimming or select a better dataset. ...
written 5 weeks ago by
Michael Dondrup ♦ 45k
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For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
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For A: Do Bad Questions Even Exist?
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For Closing Aug. 15th: PhD Position in Computational Biology (4 years), Evolution of Gene Regulation, University of Bergen, Norway
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For A: How do I find the set of a genomicrange? (same as union(gr, gr))
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For A: How do I find the set of a genomicrange? (same as union(gr, gr))
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For A: How To Extract Reads From Bam That Overlap With Specific Regions?
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For C: How To Generate Blast Database
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For C: How To Analyse Epigenetics Data Using Bioinformatics Tools?
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