User: timstuart

gravatar for timstuart
timstuart30
Reputation:
30
Status:
New User
Location:
Australia
Website:
http://timoast.github.io/
Twitter:
timoast
Last seen:
1 week, 2 days ago
Joined:
1 year, 3 months ago
Email:
t**********@gmail.com

Posts by timstuart

<prev • 5 results • page 1 of 1 • next >
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Comment: C: How to download all searched SRA result data at once?
... I don't use windows myself so I'm not 100% sure, but I think you can now run bash on windows 10...or maybe try starting docker container with ubuntu bash: `docker run -t -i ubuntu bash` https://www.docker.com/docker-windows You'll also need pigz so run `apt-get update && apt-get install p ...
written 12 weeks ago by timstuart30
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Comment: C: Identification of short insertions in genome
... I think delly and lumpy should both be able to detect indels 200-300 bp without much trouble ...
written 3 months ago by timstuart30
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Answer: A: Identification of short insertions in genome
... I'd recommend using lumpy or delly2 for small indels, rather than trying reinvent your own method https://github.com/dellytools/delly https://github.com/arq5x/lumpy-sv ...
written 3 months ago by timstuart30
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Comment: C: How to download all searched SRA result data at once?
... You just need one line per SRA accession, exactly as the file list is downloaded from the SRA. Then run the program like this: `sh download_from_sra.sh -f SraAccList.txt` ...
written 3 months ago by timstuart30
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Answer: A: How to download all searched SRA result data at once?
... Hi, I had a similar problem so wrote this script to do it, which I find is better than fastq-dump: https://github.com/timoast/ngs-tools/blob/master/download_from_sra.sh You just need to get the list of accession names from the SRA by going to that page you linked, select send to > file > for ...
written 3 months ago by timstuart30

Latest awards to timstuart

Scholar 3 months ago, created an answer that has been accepted. For A: Identification of short insertions in genome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Identification of short insertions in genome

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