User: Phil Ewels
Phil Ewels • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Sweden / Stockholm / SciLifeLab
- Website:
- http://phil.ewels.co.uk/
- Twitter:
- tallphil
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 2 years, 9 months ago
- Email:
- p*********@scilifelab.se
Bioinformatician working for the NGI Applications group at SciLifeLab in Stockholm. Interested in epigenetics. Author of MultiQC.
Posts by Phil Ewels
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Comment:
C: Bismark on sample with 2 genomes
... > I highly recommend you do not use Bismark as it is slow and in my hands prone to errors.
Interesting - in my hands I have found the opposite. BWA-meth seems to be much more permissive with its alignments than Bismark, which has caused all kinds of weird post-alignment artefacts for me in the p ...
written 3 months ago by
Phil Ewels • 30
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... Bismark comes with a tool to generate bisulfite converted genomes which you need to use before running it - `bismark_genome_preparation` (see the [docs](https://github.com/FelixKrueger/Bismark/tree/master/Docs#i-running-bismark_genome_preparation)). This creates bisulfite converted versions of your ...
written 3 months ago by
Phil Ewels • 30
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... These logs are showing the search paths that you've given, not the files that it has found / parsed. The problem is described in my other reply below - MultiQC is finding your files with no problem, but overwriting them each time as they have the same filename. ...
written 7 months ago by
Phil Ewels • 30
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... Hi Cristian,
Author of MultiQC here. The problem here is that STAR has an option to prefix log files with a sample name, giving `sample.Log.final.out`. By default, MultiQC takes this prefix as a sample name. When I wrote the module I didn't realise that if this wasn't surprised, you _just_ get `Log ...
written 7 months ago by
Phil Ewels • 30
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... As with another poster above, I wrote my own tool to handle pipelines in case it's of any interest to anyone. It's called Cluster Flow: http://ewels.github.io/clusterflow/
It doesn't tick all of your boxes, but is designed to be easy to customise and get running. It uses default cluster queue manag ...
written 2.8 years ago by
Phil Ewels • 30
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