Moderator: Ido Tamir

gravatar for Ido Tamir
Ido Tamir5.0k
Reputation:
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Location:
Austria
Last seen:
17 minutes ago
Joined:
8 years, 7 months ago
Email:
i********@imp.ac.at

Tired of missing provenance for your fastq files?

Not knowing which scales the qualities are on?

 

Handling two files for paired end reads instead of one?

 

 

Try bam files instead! A well defined specification (for biological standards). Easy to use tools.

 

Convert illumina basecalls to bam files fresh from the machine: illumina2bam https://github.com/gq1/illumina2bam

 

Posts by Ido Tamir

<prev • 312 results • page 1 of 32 • next >
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Comment: C: problem installing cutadapt
... sorry, did not read, but that is very wierd. Did you use a new conda environment? did you activate the new environment? look at $PATH, $PYTHONPATH , `which cutadapt` if there are discrepancies that would explain the problem. i.e. which version does get picked up ...
written 8 days ago by Ido Tamir5.0k
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Comment: A: problem installing cutadapt
... start using conda, it helps a bit: https://bioconda.github.io/user/install.html#install-conda ...
written 8 days ago by Ido Tamir5.0k
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Comment: C: HTseq does not generate any counts file
... https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html ...
written 4 weeks ago by Ido Tamir5.0k
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Comment: C: HTseq does not generate any counts file
... I guess you use a different python than HTseq count. Best and easiest is you switch to conda and create your own environment independent of the administrators. ...
written 4 weeks ago by Ido Tamir5.0k
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Answer: A: HTseq does not generate any counts file
... You also need pysam on the PYTHONPATH. Normally it should have been installed together with HTSeq-count automatically. Maybe more stuff is broken ... If you work on your own computer you could do this with e.g. pip install pysam https://pypi.org/project/pysam/ . You could also start working with c ...
written 5 weeks ago by Ido Tamir5.0k
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Comment: C: RNA seq library size
... the problem is not the question, but the term vague "library size". It depends on what you want to do with the estimate. For diff expression normalisation one normally uses the sum of counts in genes. If you mean the count of all the reads that came out of the sequencer for your library? Then depen ...
written 5 weeks ago by Ido Tamir5.0k
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Comment: C: ggplot second y-axis: how to specify a secondary axis if I don't want to scale m
... maybe you want something which ggplot makes difficult on purpose. The 2. axis has to be a (linear?) transformation of the 1. axis in ggplot2. this is by design, because everything else is confusing for the reader. ...
written 9 weeks ago by Ido Tamir5.0k
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Answer: A: ggplot second y-axis: how to specify a secondary axis if I don't want to scale m
... https://ggplot2.tidyverse.org/reference/sec_axis.html everything more requires you to post some easily reproducible code ...
written 9 weeks ago by Ido Tamir5.0k
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Answer: A: NGS Data Storage Best Practices (Clinical)
... You should at least store RunInfo.xml and runParameters.xml . The InterOp folder is also small but might be important at least until you are sure that the run is ok. But even the historic perspective could be interesting. It would also be nice if Illumina could get their act together so that it wo ...
written 9 weeks ago by Ido Tamir5.0k
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Comment: C: Help with awk command
... Are you sure its the last line and not the first one? Maybe the newline is wrong. Think about what the awk actually does. (edit misread statement). ...
written 3 months ago by Ido Tamir5.0k

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