User: colindaven

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colindaven260
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Posts by colindaven

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Annotate SNV (or breakpoint) data
... 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 colindaven260
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Answer: A: What platform similar to Galaxy can handle multiple batch processing of bacteria
... 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 colindaven260
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Answer: A: number of threads for cufflinks transcript assembly
... 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 colindaven260
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Answer: A: Weird fragments when aligning PE reads to duplicated genes.
... 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 colindaven260
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Comment: C: How to annotate novel SNPs using coding sequence position?
... 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 colindaven260
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Answer: A: Using long reads to find a combination of mutations
... 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 colindaven260
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Answer: A: How to annotate novel SNPs using coding sequence position?
... 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 colindaven260
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Answer: A: Functional annotation pipeline
... 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 colindaven260
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Answer: A: if i do mistake in library type parameter of trinity assembly, do i need to reas
... 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 colindaven260
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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 colindaven260

Latest awards to colindaven

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Appreciated 5 months ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Scholar 5 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 7 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
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