User: brent_wilson

gravatar for brent_wilson
brent_wilson70
Reputation:
70
Status:
Trusted
Location:
Cofactor Genomics (St. Louis, MO)
Website:
https://cofactorgenomi...
Last seen:
1 month ago
Joined:
1 year, 3 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 • 16 results • page 1 of 2 • next >
0
votes
0
answers
214
views
0
answers
Comment: C: Different length reads and How to handle?
... Since the two read lengths likely came from different libraries, I would be concerned about mixing and matching. Can you provide more context? ...
written 12 weeks ago by brent_wilson70
0
votes
0
answers
146
views
0
answers
Exosomal miRNA vs cellular miRNA alignment rates
... Does anyone have experience with the relative alignment rates to miRNA from exosomal sources vs from cellular sources? I have seen some data with quite low alignment rates for exosomal miRNA and I didn't know if this was consistent with other's experience. ...
alignment mirna written 3 months ago by brent_wilson70
0
votes
0
answers
459
views
0
answers
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 months ago by brent_wilson70
0
votes
1
answer
278
views
1
answers
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 6 months ago by brent_wilson70
0
votes
0
answers
352
views
0
answers
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 6 months ago by brent_wilson70
1
vote
1
answer
371
views
1
answers
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 9 months ago by brent_wilson70
0
votes
2
answers
611
views
2
answers
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 9 months ago by brent_wilson70
2
votes
2
answers
611
views
2
answers
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 9 months ago by brent_wilson70
0
votes
1
answer
653
views
1
answers
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 12 months ago by brent_wilson70
0
votes
1
answer
315
views
1
answers
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 12 months ago by brent_wilson70

Latest awards to brent_wilson

Scholar 14 months ago, created an answer that has been accepted. For A: How to find % alignment of total reads to genic region?
Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1063 users visited in the last hour