User: bruce.moran

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bruce.moran370
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Posts by bruce.moran

<prev • 85 results • page 1 of 9 • next >
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Answer: A: CNA vs mRNA Expression level
... [This paper][1] might help, it deals with CNA, mRNA and proteome, and presents an 'attenuation expression signature' for genes that are unaffected by CNV, possibly due to degradation of a rate-limiting complex-partner. Probably goes beyond your scope, but some useful ideas (at least for me!). [ ...
written 4 months ago by bruce.moran370
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Comment: C: Isolating reads from specific region from bam file
... Thanks, I find it particularly useful for IGV or other viewers, instead of trying to load a whole BAM locally. ...
written 4 months ago by bruce.moran370
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Comment: C: What's fascinating about Bioinformatics for potential students?
... This is why I wanted to train in bioinformatics: it is useful to all aspects/fields of biology. So with that background you can really slot in anywhere. As @me says, commercial/industry is available too therefore decent money, more opportunity outside academia (and not necessarily biology, a lot of ...
written 5 months ago by bruce.moran370
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Comment: C: Alignment of exome to gene set
... See: [https://www.biostars.org/p/7549/][1] The short answer to your question is 'no'. You can use regions for mutation calling to reduce to your 50 genes though (e.g. the -L flag if calling mutations with GATK) [1]: https://www.biostars.org/p/7549/ ...
written 6 months ago by bruce.moran370
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Comment: C: How to rename chromosome names in GTF file?
... You could redirect to a new file and use that, no real need for -i sed 's/CHROMOSOME_//g' celegans.gtf > celegans.noChr.gtf ...
written 7 months ago by bruce.moran370
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Answer: A: Dealing with multimapping reads in featureCounts
... The only way to know if multi-mapping reads make a difference to a DE analysis is to run it with and without them. In my experience, it depends on the study. Cell lines seem more robust, tissue samples less, but this may be due to inherent biological variation. There are several ways to use mulit-ma ...
written 7 months ago by bruce.moran370
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Comment: C: CWL rerunning completed output
... Thanks Michael, appreciate your input. ...
written 7 months ago by bruce.moran370
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Comment: C: CWL rerunning completed output
... Only have a few months using Make so was assessing the alternatives. I read your paper on this, so appreciate your experience. Do you have anything written on your own preferred solution, especially for production? ...
written 7 months ago by bruce.moran370
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Comment: C: CWL rerunning completed output
... OK, very interesting. Your issue on Github is only a few months old, and caching is described as 'experimental' in the response, so I don't think this is going to be useful for production work I will be doing. Hopefully this will be part of next updates. Many thanks for the input, and the example. ...
written 7 months ago by bruce.moran370
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5 follow
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CWL rerunning completed output
... I like CWL, and would like to use it in a production setting. I am coming from a Make approach, whereby output is not remade unless datestamps of input determine this to be necessary. I cannot find any documentation on this aspect for CWL. I have read the 'Gentle Intro' twice end-to-end thinking thi ...
common workflow language cwl written 7 months ago by bruce.moran370 • updated 7 months ago by well30960

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