Moderator: Brian Bushnell

gravatar for Brian Bushnell
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

<prev • 1,850 results • page 1 of 185 • next >
0
votes
1
answer
890
views
1
answers
Comment: C: Demultiplex paired-end reads with dual primers and barcodes
... "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 Bushnell14k
0
votes
2
answers
110
views
2
answers
Answer: A: Organism name from accession numbers
... 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 Bushnell14k
0
votes
1
answer
168
views
1
answers
Comment: C: Maintaning internal or private installation of Biostar or a similar Q&A site
... Oh, I misinterpreted what you were asking for. Thanks for clarifying! ...
written 3 days ago by Brian Bushnell14k
0
votes
1
answer
168
views
1
answers
Comment: C: Maintaning internal or private installation of Biostar or a similar Q&A site
... 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 Bushnell14k
0
votes
1
answer
132
views
1
answers
Comment: C: (ERR): bowtie2-align exited with value 1
... TopHat is obsolete and the developers no longer recommend that anyone use it.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 Bushnell14k
0
votes
1
answer
228
views
1
answers
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 Bushnell14k
0
votes
0
answers
150
views
0
answers
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 Bushnell14k
0
votes
2
answers
104
views
2
answers
Answer: A: How to add the suffix if the entries are the same in fasta file
... 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 Bushnell14k
0
votes
0
answers
150
views
0
answers
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 Bushnell14k
0
votes
1
answer
113
views
1
answers
Comment: C: Filtering of RNA fastq files prior to aligment
... 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 Bushnell14k

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
Appreciated 12 days ago, created a post with more than 5 votes. For A: Duplicates on Illumina
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
Appreciated 21 days ago, created a post with more than 5 votes. For A: Duplicates on Illumina
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
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Duplicates on Illumina
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
Scholar 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1865 users visited in the last hour