User: colindaven
colindaven • 260
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Posts by colindaven
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... You could do it in R with the package GenomicRanges, but I prefer the command line tool bedtools.
It's easy to install using bioconda, and the the command bedtools intersect should be helpful.
...
written 1 day ago by
colindaven • 260
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... This is not easy, but is possible in Galaxy with collections. There was a talk at the galaxy conference about it.
See the abstract and linked slides in the following.
https://gcc2017.sched.com/event/BH73/galaxy-at-scale-analyzing-thousands-of-single-cell-transcriptomes
You will probably end up w ...
written 2 days ago by
colindaven • 260
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... Cufflinks does have a -p argument, alternatively --no-of-threads
cufflinks v2.2.1
linked against Boost version 104700
Usage: cufflinks [options]
General Options:
-o/--output-dir write all output files to this directory [ default: ./ ]
-p/--nu ...
written 4 days ago by
colindaven • 260
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... Can't you just exclude "improper pairs" with an insert size longer than the expected ( 300bp?) ?
bamtools filter (easy to install via bioconda) should be able to do this.
Also check your insert size distributions statistically for this region after filtering
...
written 8 days ago by
colindaven • 260
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... Sounds like you'll have to convert to a standard format. Try a minimal VCF version, it's probably easiest and best documented (in my experience). You probably don't need the INFO or GT columns. Good luck. ...
written 10 days ago by
colindaven • 260
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... Whatshap or Phaser https://github.com/secastel/phaser are on the right track here.
However I think these problems a) only work with maximal diploid ploidy and b) will struggle with nanopore reads.
I would first correct the reads by running canu on them, then use the resultant corrected fastq for f ...
written 10 days ago by
colindaven • 260
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... I would recall your SNPs in a standard format - VCF. Then use Annovar, Ensembl VEP or snpEff to call. Otherwise you're going to have to script it with biopython or similar. That's going to be a world of pain considering it's essentially a solved problem. ...
written 10 days ago by
colindaven • 260
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... I like Interproscan for functional annotation. It is surprisingly quick and easy to use, as long as you don't try to run it on a cluster.
https://github.com/ebi-pf-team/interproscan
...
written 11 days ago by
colindaven • 260
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... It might be low quality data, but please tell us step by step what was done exactly. Also, you can run it through a trinity workflow for example on Galaxy main.
How many reads do you have ?
Another assembler - CLC is easy and quite good, or soapdenovo-trans has a decent reputation - might help too ...
written 11 days ago by
colindaven • 260
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Comment:
C: SNPs Calling Tools
... Hi Brian,
I created this page.
https://www.biostars.org/p/262972/
I can't comment on general variant calling very much since this is just for high-depth mitochondria - but the next project is bacterial genomes with PacBio where SNVs should also be called, so maybe I can add more then.
Colin ...
written 11 days ago by
colindaven • 260
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