User: Phil Ewels
Phil Ewels • 470
- Reputation:
- 470
- Status:
- Trusted
- Location:
- Sweden / Stockholm / SciLifeLab
- Website:
- http://phil.ewels.co.uk/
- Twitter:
- tallphil
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 week, 3 days ago
- Joined:
- 5 years, 1 month 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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... Ok great! Glad you got it sorted. No problem at all :) ...
written 12 days ago by
Phil Ewels • 470
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... Hi [ATpoint][1],
I'm a little confused - doesn't the backslash in the command escape the whitespace? Usually paths with `two\ words` are fine (`two words` would not be). What error do you see? In the [post reporting this problem][2] I can only see paths *without* the backslash escape, so I can unde ...
written 15 days ago by
Phil Ewels • 470
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Answer:
A: Installing MultiQC on Ubuntu
... See https://multiqc.info/docs/#installing-multiqc
> Before we start - a quick note that using the system-wide installation of Python is **not** recommended. This often causes problems and it's a little risky to mess with it. If you find yourself prepending `sudo `to any MultiQC commands, take a ...
written 7 weeks ago by
Phil Ewels • 470
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... # This step is necessary since the input files
# must be loaded into the working directory as there
# is no way to specify the input file directly on the
# command line.
Note that you can give specific file paths to MultiQC if you want to, it doesn't _have_ to be a directory. The fo ...
written 7 weeks ago by
Phil Ewels • 470
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... 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 9 months ago by
Phil Ewels • 470
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... 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 9 months ago by
Phil Ewels • 470
• updated
6 weeks ago by
psschlogl • 20
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... 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 9 months ago by
Phil Ewels • 470
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... 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 12 months ago by
Phil Ewels • 470
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... 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 12 months ago by
Phil Ewels • 470
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... 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 12 months ago by
Phil Ewels • 470
Latest awards to Phil Ewels
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For System developer at NGI Stockholm Sequencing Facility, SciLifeLab Sweden
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: Converting FASTQC Reports to PDF
Popular Question
9 months ago,
created a question with more than 1,000 views.
For sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Scholar
9 months ago,
created an answer that has been accepted.
For A: Converting FASTQC Reports to PDF
Scholar
9 months ago,
created an answer that has been accepted.
For A: MultiQC extra_fn_clean_exts for specific module
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Converting FASTQC Reports to PDF
Appreciated
9 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
12 months ago,
created an answer that has been accepted.
For A: Converting FASTQC Reports to PDF
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Converting FASTQC Reports to PDF
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5.1 years ago,
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