User: brent_wilson

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brent_wilson60
Reputation:
60
Status:
Trusted
Location:
Cofactor Genomics (St. Louis, MO)
Website:
https://cofactorgenomi...
Last seen:
5 days, 6 hours ago
Joined:
7 months, 3 weeks 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 • 11 results • page 1 of 2 • next >
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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 4 weeks 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 weeks 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 weeks 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 4 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 4 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 6 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 6 months ago by brent_wilson60
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Answer: A: Reads length mouse RNA-seq
... Hi Pisi, We handle a lot of RNA-Seq, and read length (really fragment length) is important for crossing the exon-exon junction as you mention. We definitely recommend paired-end reads for this application (though paired-end Illumina reads will also work for differential expression applications). H ...
written 6 months ago by brent_wilson60
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Answer: A: What Does Samtools Flagstat Results Mean?
... Sometimes the cause of massive amounts of improper pairing is due to your reads being out of order in the reads files (assuming you have separate R1 and R2 files). This can easily happen if you are filtering out reads from your files and both reads of a pair are not eliminated (ex: R2 loses read #1 ...
written 6 months ago by brent_wilson60
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Answer: A: extracting reads from fastq file based on read_id
... For bash, I would use a nice one-liner: for x in $(cat tmp); do reads.fastq | grep $x -A 3; done Of course you can redirect to wherever you want: for x in $(cat tmp); do reads.fastq | grep $x -A 3; done > tmp2 I hope that this helps! Brent Wilson, PhD | Project Scientist | Cofactor Genomic ...
written 7 months ago by brent_wilson60

Latest awards to brent_wilson

Scholar 6 months ago, created an answer that has been accepted. For A: How to find % alignment of total reads to genic region?
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.

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