User: Phil Ewels

gravatar for Phil Ewels
Phil Ewels470
Reputation:
470
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Trusted
Location:
Sweden / Stockholm / SciLifeLab
Website:
http://phil.ewels.co.uk/
Twitter:
tallphil
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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

<prev • 29 results • page 1 of 3 • next >
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Comment: C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
... Ok great! Glad you got it sorted. No problem at all :) ...
written 12 days ago by Phil Ewels470
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Comment: C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
... 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 Ewels470
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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 Ewels470
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Answer: A: ask for a CWL script to perform FASTQC to get quality control files, then use th
... # 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 Ewels470
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Comment: C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
... 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 Ewels470
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Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
... 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 ...
sra fastq tool sequence-read-archive download written 9 months ago by Phil Ewels470 • updated 6 weeks ago by psschlogl20
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Answer: A: MultiQC extra_fn_clean_exts for specific module
... 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 Ewels470
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Answer: A: How do you use MultiQC on FastQC files taken from SRA files?
... 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 Ewels470
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Answer: A: Difference in duplicate number with samtools flagstat and multiqc/fastqc
... 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 Ewels470
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Comment: C: How to extract mapping features of multiple samples in one output?
... 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 Ewels470

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
Autobiographer 5.1 years ago, has more than 80 characters in the information field of the user's profile.

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