Moderator: Brian Bushnell

gravatar for Brian Bushnell
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Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
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Joined:
2 years, 8 months ago
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I like to program in Java.

Posts by Brian Bushnell

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Comment: C: How do I reduce the length of a contig?
... The best approach is to use a different program that does not have such a strange and arbitrary limitation. But if you need to observe a 500kbp limit, manually separate them, rather than trying to find parameters that make SPAdes give you a bad assembly. You can use BBMap like this: reformat. ...
written 2 days ago by Brian Bushnell13k
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Comment: C: align spike in database
... With such short sequences, I think kmer-matching will probably work better than alignment... are those the full length of the spike-ins? ...
written 2 days ago by Brian Bushnell13k
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Comment: C: fasta files: keep only lines containing certain characters + the respective sequ
... Whether or not you can do this depends on the contents of the file, and how precise you need to be. In the general case, no, it is not possible. I suggest you post the headers of some of your sequences, along with as much other data as possible. And clarify whether you wish to separate sequences ...
written 3 days ago by Brian Bushnell13k
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Comment: C: How to find the mapping quality (mapQ) score of a variant
... I'd like to note, though, that some VCF files give an average MAPQ and base quality for a given variant, and some don't. VCF is extensible, so it's not really a format, but more of a format for formats. As such, you never know what might be inside a VCF, and it's never possible to access the infor ...
written 3 days ago by Brian Bushnell13k
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Comment: C: multiprocesses vs multithreads in application
... Linux can handle multithreaded processes fine, but it's still up to the authors of a user program to handle threading as well; you can't give a singlethreaded program to Linux and expect Linux to make it multithreaded, any more than you can expect a good mechanic to make a 1-cylinder engine into a 4 ...
written 3 days ago by Brian Bushnell13k
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Comment: C: multiprocesses vs multithreads in application
... Personally, I never worry about allocating too many threads in Linux... when testing multithreaded processes in Windows, I routinely see the computer become unresponsive if I use all logical cores without explicitly setting a reduced priority (at which point it's hard to kill the process since ever ...
written 3 days ago by Brian Bushnell13k
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Comment: C: How to find the mapping quality (mapQ) score of a variant
... If a read aligns equally well to two locations, both locations should get the same MAPQ (in this case, 3 or less). So you should not be able to distinguish between a read originating from a gene or pseudogene except in the regions where they differ. ...
written 3 days ago by Brian Bushnell13k
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Comment: C: FASTQC Per base sequence quality fail after removal of adaptors
... By "robust quality trimming" I mean using a quality-trimming method that takes into account internal bases rather than the standard method of trimming bases until one is encountered that has a quality score above some threshold (which, I believe, is fastx's method). Note that quality-trimming and a ...
written 4 days ago by Brian Bushnell13k
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Comment: C: FASTQC Per base sequence quality fail after removal of adaptors
... I'm not entirely sure what fastx is doing internally, but I'd like to note that: When you have insert size shorter than read length (as in small RNA), and if you have fairly low-quality data, then: If you perform adapter-trimming only, you will enrich for low-quality tails because the high-quality ...
written 4 days ago by Brian Bushnell13k
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Answer: C: align spike in database
... Depending on how long and specific your spike-ins are, I recommend using BBMap's Seal which can both remove and quantify them using kmer-matching. For example: seal.sh in=reads.fq ref=spikeins.fa pattern=spikein_%.fq outu=clean.fq stats=stats.txt k=31 ...
written 4 days ago by Brian Bushnell13k

Latest awards to Brian Bushnell

Commentator 4 days ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Teacher 6 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 10 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 10 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 11 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 12 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 12 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 12 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 15 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 18 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 20 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 26 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
Scholar 29 days ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Teacher 29 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
Scholar 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Scholar 4 weeks ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Extract A Subset Of Reads In Fastq Using An Id List?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training

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