User: Vince Buffalo
Vince Buffalo • 460
- Reputation:
- 460
- Status:
- Trusted
- Location:
- Davis, CA
- Website:
- http://bioinformatics....
- Last seen:
- 4 years, 6 months ago
- Joined:
- 10 years, 1 month ago
- Email:
- v********@gmail.com
Author of Bioinformatics Data Skills and aspiring population geneticist.
Posts by Vince Buffalo
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1
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... I'll let others answer your question so you get honest feedback, but I'm happy to answer any questions about the book. Do note that Bioinformatics Data Skills is an intermediate book — it assumes readers have learned a scripting language. This prerequisite allows me to dive into computational and da ...
written 4.7 years ago by
Vince Buffalo • 460
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2
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2.6k
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... Yup, the final print and ebook versions are out! I'd be happy to answer questions about the text too.
...
written 4.7 years ago by
Vince Buffalo • 460
4
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7
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4.4k
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... I share this frustration with too, which is why I am writing this book. It's the book I wish I had when learning bioinformatics. It's an intermediate book (assumes readers know a bit of a scripting language), as this is what is lacking in current bioinformatics books. Many biologists learn a scripti ...
written 6.2 years ago by
Vince Buffalo • 460
• updated
3 months ago by
RamRS ♦ 26k
2
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2.5k
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... Hi knhai45,
I just made the correction Heng Li's awesome toolkit. Here's the pull request but in the meantime you could use my version.
...
written 6.8 years ago by
Vince Buffalo • 460
1
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1
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6.4k
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... I wrote something for it here: https://github.com/vsbuffalo/findorf/blob/master/findorf/orfprediction.py but this may be too project-specific. It handles some other cases though which you may find interesting.
...
written 6.8 years ago by
Vince Buffalo • 460
0
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7
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5.8k
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7
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... Intentional; showing readers how to do it in FASTQ allows them to extend it to FASTA. Anyone that can't adapt this to FASTA probably shouldn't be copying and pasting commands from the internet into their shells.
...
written 7.2 years ago by
Vince Buffalo • 460
6
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5.8k
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... Or, use bioawk, which deals with gzipped files and FASTQ natively. I recommend it more than rolling your own FASTQ parser each time.
For example:
bioawk -cfastx '{if (length($seq) <= 100) {print "@"$name"\n"$seq"\n+\n"$qual}} ' file.fq.gz
Note: this only uses FASTQ names (before the first sp ...
written 7.2 years ago by
Vince Buffalo • 460
0
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3
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2.4k
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3
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... Absolutely! It's astounding how accessible this text is. And it's so well-written that it can function as more than a reference. ...
written 8.9 years ago by
Vince Buffalo • 460
8
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73
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33k
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73
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... One mistake: not looking to see that the 0x4 bit in the bitflag column of a SAM (or BAM) file indicates the entry is mapped. RNAME, CIGAR, and POS may be set to something non-null (an actual string!) but these are not meaningful if the 0x4 flag says the read is unmapped.
...
written 8.9 years ago by
Vince Buffalo • 460
4
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3
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6.4k
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3
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... I think that trifecta is missing biology and statistics. ...
written 9.0 years ago by
Vince Buffalo • 460
Latest awards to Vince Buffalo
Autobiographer
4.7 years ago,
has more than 80 characters in the information field of the user's profile.
Appreciated
6.1 years ago,
created a post with more than 5 votes.
For A: How To Discard Sequences Longer Than N Nucleotides ?
Good Answer
6.1 years ago,
created an answer that was upvoted at least 5 times.
For A: How To Discard Sequences Longer Than N Nucleotides ?
Good Answer
6.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Trimming Algorithm
Supporter
6.1 years ago,
voted at least 25 times.
Commentator
6.1 years ago,
created a comment with at least 3 up-votes.
For C: What'S The Best Generic Scripting Tool For Bioinformatics?
Commentator
6.1 years ago,
created a comment with at least 3 up-votes.
For C: Best Way To Learn Bioinformatics For System Level Programmers.
Teacher
6.1 years ago,
created an answer with at least 3 up-votes.
For A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Teacher
6.1 years ago,
created an answer with at least 3 up-votes.
For A: How To Discard Sequences Longer Than N Nucleotides ?
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