User: Phil Ewels

gravatar for Phil Ewels
Phil Ewels30
Reputation:
30
Status:
New User
Location:
Sweden / Stockholm / SciLifeLab
Website:
http://phil.ewels.co.uk/
Twitter:
tallphil
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Google Scholar Page
Last seen:
3 days, 22 hours ago
Joined:
2 years, 6 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

<prev • 5 results • page 1 of 1 • next >
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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 days ago by Phil Ewels30
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Answer: A: Bismark on sample with 2 genomes
... 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 days ago by Phil Ewels30
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Comment: C: Running multiQC on more than one file Log.final.out from STAR
... 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 4 months ago by Phil Ewels30
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Answer: A: Running multiQC on more than one file Log.final.out from STAR
... 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 4 months ago by Phil Ewels30
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Answer: A: Workflow management software for pipeline development in NGS
... 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 2.5 years ago by Phil Ewels30

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