Moderator: Brian Bushnell
Brian Bushnell ♦ 13k
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- Walnut Creek, USA
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- http://sourceforge.net...
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- b********@lbl.gov
I like to program in Java.
Posts by Brian Bushnell
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... 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 Bushnell ♦ 13k
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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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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... 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 Bushnell ♦ 13k
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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 Bushnell ♦ 13k
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For C: bioinformatics basic training
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For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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For A: all-mapper for differently trimmed mates
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For A: all-mapper for differently trimmed mates
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For A: all-mapper for differently trimmed mates
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For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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For A: all-mapper for differently trimmed mates
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For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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For A: RNA-seq differential expression analysis, which aligner to choose between BWA/to
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For A: How To Extract A Subset Of Reads In Fastq Using An Id List?
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For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
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For C: bioinformatics basic training
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