Moderator: Brian Bushnell
Brian Bushnell ♦ 14k
- Reputation:
- 13,690
- Status:
- Trusted
- Location:
- Walnut Creek, USA
- Website:
- http://sourceforge.net...
- Last seen:
- 10 hours ago
- Joined:
- 2 years, 10 months ago
- Email:
- b********@lbl.gov
I like to program in Java.
Posts by Brian Bushnell
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... "mm" means "maskmiddle". It essentially allows a single mismatch when doing kmer-matching, as long as that mismatch is in the middle of the kmer. So it increases sensitivity. But if you need exact matches only, set it to false as in this example. ...
written 20 hours ago by
Brian Bushnell ♦ 14k
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... You can also get the organism from accessions like this:
http://taxonomy.jgi-psf.org/tax/accession/ELW65244.1,XP_013802631.1 ...
written 1 day ago by
Brian Bushnell ♦ 14k
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... Oh, I misinterpreted what you were asking for. Thanks for clarifying! ...
written 3 days ago by
Brian Bushnell ♦ 14k
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... Biostar and Stack Exchange, etc. are not workflows and you should assume any answer needs to be modified to suit your situation. They are also not private, internal, or secret in any way. They are recommendations to people who need advice. Of course you can use this advice however you want. But ...
written 3 days ago by
Brian Bushnell ♦ 14k
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... TopHat is obsolete and the developers no longer recommend that anyone use it. I suggest you use a different aligner such as Star or BBMap. ...
written 3 days ago by
Brian Bushnell ♦ 14k
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Comment:
C: Remove gap from files
... This question is unrelated to Perl or Blast so I removed those tags. ...
written 3 days ago by
Brian Bushnell ♦ 14k
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150
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Comment:
C: species relative abundance
... This sounds like a problem needing a customized solution. I think you need to talk to the bioinformatician working with you... ...
written 3 days ago by
Brian Bushnell ♦ 14k
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... With BBMap's reformat.sh:
reformat.sh in=file.fa out=fixed.fa uniquenames
That appends "_2", "_3", etc to the second and 3rd instance of a name. The first time a name occurs it will be unaffected. ...
written 4 days ago by
Brian Bushnell ♦ 14k
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Comment:
C: species relative abundance
... If you already have the abundance data in Excel... then this is not really a bioinformatics question. Generally, you go to the "Insert" tab, draw a rectangle around the data, select "Column" and pick a chart type.
Try this for more information:
https://blog.hubspot.com/marketing/how-to-build-exc ...
written 4 days ago by
Brian Bushnell ♦ 14k
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... To make this clear to future readers, BBDuk is open-source, available [here][1], and free for all uses.
[1]: https://sourceforge.net/projects/bbmap/ ...
written 4 days ago by
Brian Bushnell ♦ 14k
Latest awards to Brian Bushnell
Scholar
4 days ago,
created an answer that has been accepted.
For A: all-mapper for differently trimmed mates
Teacher
4 days ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator
12 days ago,
created a comment with at least 3 up-votes.
For C: Benchmark - Comparison of Different NGS Mappers
Popular Question
12 days ago,
created a question with more than 1,000 views.
For BBSketch - A Tool for Rapid Sequence Comparison
Teacher
20 days ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar
21 days ago,
created an answer that has been accepted.
For A: all-mapper for differently trimmed mates
Teacher
21 days ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator
23 days ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Commentator
23 days ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Commentator
25 days ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Teacher
25 days ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher
27 days ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Good Answer
4 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Duplicates on Illumina
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4 weeks ago,
created an answer that has been accepted.
For A: all-mapper for differently trimmed mates
Appreciated
5 weeks ago,
created a post with more than 5 votes.
For A: Extending ends of sequences with the help of reads?
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: all-mapper for differently trimmed mates
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: all-mapper for differently trimmed mates
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: all-mapper for differently trimmed mates
Commentator
8 weeks ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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