User: Heather Ward

gravatar for Heather Ward
Heather Ward50
Reputation:
50
Status:
New User
Location:
Guelph, ON
Last seen:
22 hours ago
Joined:
5 months, 1 week ago
Email:
h*************@gmail.com

I am a bioinformatician at DNAstack, a Toronto-based genomics company. I write workflows using the Workflow Description Language (WDL) that execute in the Cloud.

My background is in biochemistry and evolutionary genetics.

Posts by Heather Ward

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Comment: C: Filter DNA sequence in FASTA file by minimum length and redirect sequences that
... Yes, this would work, however it's generally bad practice because doing this will destroy your input file. It would be best to save your output as a new file in case something goes wrong in your program and your output isn't what you'd expect. For example, imagine in the codeblock you posted there ...
written 7 days ago by Heather Ward50
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Answer: A: converting fast5 to fasta failed
... It may be that your files don't have the type of reads that ```best``` extracts. Have you tried using some of the other types, for example ```2D```, or no type at all? If that outputs something, it's likely that your file doesn't have any reads that match the type ```best```, which doesn't seem to m ...
written 7 days ago by Heather Ward50
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Answer: A: Filter DNA sequence in FASTA file by minimum length and redirect sequences that
... You've got some problems in there - for example, ```seq = np.asarray(list(data))``` seq is only going to contain the last line of the fasta file, not every sequence. Try going back through your code line by line and think about what the data variable gets filled with during each iteration, and why t ...
written 7 days ago by Heather Ward50

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Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Filter DNA sequence in FASTA file by minimum length and redirect sequences that
Autobiographer 4 weeks ago, has more than 80 characters in the information field of the user's profile.

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