User: Phil Ewels

gravatar for Phil Ewels
Phil Ewels420
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 >
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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 4 months ago by Phil Ewels420
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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 4 months ago by Phil Ewels420
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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 4 months ago by Phil Ewels420
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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 7 months ago by Phil Ewels420
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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 7 months ago by Phil Ewels420
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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 7 months ago by Phil Ewels420
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Answer: A: Converting FASTQC Reports to PDF
... 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 Ewels420
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Job: System developer at NGI Stockholm Sequencing Facility, SciLifeLab Sweden
... 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 ...
automation sysadmin job facility developer written 20 months ago by Phil Ewels420
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Comment: C: How to calculate the percent of methylated cytosines.
... If you post a link to the paper that would help to clarify the question :) ...
written 22 months ago by Phil Ewels420
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Comment: C: How to calculate the percent of methylated cytosines.
... 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 Ewels420

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.

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