User: Phil Ewels
Phil Ewels • 420
- Reputation:
- 420
- Status:
- Trusted
- Location:
- Sweden / Stockholm / SciLifeLab
- Website:
- http://phil.ewels.co.uk/
- Twitter:
- tallphil
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 months, 2 weeks ago
- Joined:
- 4 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
<prev
• 25 results •
page 1 of 3 •
next >
1
vote
0
answers
724
views
0
answers
... Nice idea and great tutorial! I've just added this functionality - it would be great if you could have a look and make sure that I haven't made any errors.. Note that I added an option to append a `mv` command to rename the files. I've never used Aspera myself, so I hope this actually works! ...
written 4 months ago by
Phil Ewels • 420
24
votes
0
answers
724
views
14 follow
0
answers
... Hi all,
As a fun little side project I've made a web tool to find runs on the NCBI Sequence Read Archive (SRA) and fetch the download URLs for these. You can do all of this in a couple of clicks, hopefully quite a bit easier than navigating the main SRA pages.
In addition to getting the SRA links ...
written 4 months ago by
Phil Ewels • 420
3
votes
1
answer
198
views
1
answers
... Hi Rick,
That's a great question and interesting use case. I don't think that it's possible to do this in MultiQC currently, but it would be a nice idea and I don't think it would be too difficult to implement.
I've made an issue here to remind me to add it the next time I get a chance to work on ...
written 4 months ago by
Phil Ewels • 420
0
votes
1
answer
693
views
1
answers
... See the MultiQC documentation about how MultiQC finds input files here: https://multiqc.info/docs/#module-search-patterns
In short, as @genomax says in the comment above, MultiQC uses the default FastQC zip and data filenames as a search pattern. But these can be customised if required. As to how b ...
written 7 months ago by
Phil Ewels • 420
1
vote
2
answers
954
views
2
answers
... I think that samtools flagstats tells you about the flagged duplicates. You need to mark these duplicate reads first, for example by running Picard MarkDuplicates. If you then run `samtools flagstats` again it should give you a more realistic figure :)
FastQC uses the raw FastQ sequences instead of ...
written 7 months ago by
Phil Ewels • 420
2
votes
1
answer
351
views
1
answers
... Correct! If you forget, you can always run `samtools stats` on your aligned BAM file, which will give you a file to feed to MultiQC for a % alignment plot. ...
written 7 months ago by
Phil Ewels • 420
4
votes
2
answers
547
views
2
answers
... The problem is that MultiQC plots are by default rendered as interactive JavaScript objects. These aren't traditional graphics and tend to not do well with HTML conversion tools such as the one you're trying. MultiQC can render static image plots though, using the option `--flat`. There's also a tem ...
written 7 months ago by
Phil Ewels • 420
0
votes
0
answers
894
views
0
answers
... We are looking for a system administrator and developer to join our production team to develop and maintain informatics solutions handling the production’s internal data flow. The job will include development of automated solutions for processing Next Generation Sequencing (NGS) data and extensive s ...
written 20 months ago by
Phil Ewels • 420
0
votes
1
answer
1.2k
views
1
answers
... If you post a link to the paper that would help to clarify the question :) ...
written 22 months ago by
Phil Ewels • 420
0
votes
1
answer
1.2k
views
1
answers
... If you want for all Cytosines, not context specific (CpG / CHG / CHH as printed in the report) just add the numbers:
* Total C's analysed `1218062196`
* Methylated C's in CpG context `31593318`
* Methylated C's in CHG context `1525159`
* Methylated C's in CHH context `3319601`
```
( (31593318 + 15 ...
written 22 months ago by
Phil Ewels • 420
Latest awards to Phil Ewels
Appreciated
4 months ago,
created a post with more than 5 votes.
For sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Scholar
7 months ago,
created an answer that has been accepted.
For A: Converting FASTQC Reports to PDF
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Converting FASTQC Reports to PDF
Autobiographer
4.8 years ago,
has more than 80 characters in the information field of the user's profile.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 878 users visited in the last hour