User: brent_wilson

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brent_wilson60
Reputation:
60
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Location:
Cofactor Genomics (St. Louis, MO)
Website:
https://cofactorgenomi...
Last seen:
1 day, 13 hours ago
Joined:
12 months ago
Email:
b***********@cofactorgenomics.com

Project Scientist for Cofactor Genomics 

I handle Sales, Customer Support and Project Management for Cofactor

My background is Computational Biology and (before that) Computational Chemistry 

Posts by brent_wilson

<prev • 14 results • page 1 of 2 • next >
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... Are they mapped in proper pairs when you check the flags? If you have a lot of improper pairing, this suggests a technical issue. Brent Wilson, PhD | Project Scientist | Cofactor Genomics 4044 Clayton Ave. | St. Louis, MO 63110 | tel. 314.531.4647 Catch the latest from Cofactor on our blog. ...
written 5 weeks ago by brent_wilson60
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Comment: C: sam to bam conversion
... You have to be careful with pipes and redirects when converting between SAM and BAM. Don't clip off anything (such as the header) that may be needed for a complete file. Brent Wilson, PhD | Project Scientist | Cofactor Genomics 4044 Clayton Ave. | St. Louis, MO 63110 | tel. 314.531.4647 Catch th ...
written 9 weeks ago by brent_wilson60
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Comment: C: PacBio Fastq file
... As genomax said, you'll want to dig deeper to make sure you are working with consensus sequence from the subreads. There are plenty of resources for working from .bax.h5 files: https://www.biostars.org/p/130590/ Brent Wilson, PhD | Project Scientist | Cofactor Genomics 4044 Clayton Ave. | St. Lou ...
written 11 weeks ago by brent_wilson60
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Answer: A: Low alignment rating
... I haven't used Trimmomatic, but sometimes trimming programs can cause your forward and reverse reads files to get out of synch. That is, if a read is removed from R2 but not R1, then the aligner will fail to align a huge percentage because nearly everything will be aligned without a proper pair. I ...
written 5 months ago by brent_wilson60
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Comment: C: Alternative to BLASR ?
... I would have, but everything is saved over at my previous position where I can't access it anymore. I do remember looking at the identity and coverage of each hit and using dot plots to train the parameters. ...
written 5 months ago by brent_wilson60
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Answer: A: Alternative to BLASR ?
... I have had much better luck for PACBIO alignment with BLAT, followed by some filtering for "true" alignments (alignment length, number of matches, etc.). It took a bit of work to set the parameters, and I haven't dealt with it in awhile, but it worked well for finding alignments (even for partial h ...
written 5 months ago by brent_wilson60
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Answer: A: Get all intronic regions from a generic GTF file
... Hi Alessandro, Here are a couple relevant links that may be useful: If you can use UCSC, rather than be forced to use a GTF file: https://www.biostars.org/p/13290/ A little more detail on a manual solution is here: https://biostar.usegalaxy.org/p/6453/ And some basic information on GTF parsing i ...
written 8 months ago by brent_wilson60
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Answer: A: problem in CAP - miRSeq
... Hi rs544, I'm not sure this is really enough information to answer your question. It could be any number of things. Maybe CAP doesn't have some permissions it needs, or you may need to index the reference file with Bowtie first. Just a couple of guess, since I don't have much to go on. Good luc ...
written 8 months ago by brent_wilson60
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Answer: A: How to find % alignment of total reads to genic region?
... Something similar has been covered previously: https://www.biostars.org/p/48719/ Short answer, Samtools has the functionality to extract a few known positions quite easily. For the larger, more scalable solution, look to: https://www.biostars.org/p/98407/ Brent Wilson, PhD | Project Scienti ...
written 10 months ago by brent_wilson60
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Answer: A: RNA sequencing depth for downstream proteomics
... The quality of the assembly may not always depend upon the number of reads used. One thing that makes a large difference in the quality of the assembly is the use of DSN treatment to normalize the number of transcripts in the sample. Adding more reads will usually help with the assembly quality, b ...
written 10 months ago by brent_wilson60

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Scholar 10 months ago, created an answer that has been accepted. For A: How to find % alignment of total reads to genic region?
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