User: jean.elbers

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jean.elbers1.1k
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Posts by jean.elbers

<prev • 150 results • page 1 of 15 • next >
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Answer: A: Create Chain File for Converting Genome Coordinates
... In that post you mention, there is `flo` https://github.com/wurmlab/flo, which I recommend and can also liftover GFF files. ...
written 21 hours ago by jean.elbers1.1k
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Comment: C: MaSuRCA, pre-processing and post-assembly improvements
... I haven't used `MaSuRCA`, but it makes sense to do quality and adapter trimming of the Illumina reads before inputting them into the `MaSuRCA` pipeline. I am not sure sure what to advise if you should do polishing or gap closing, but it is worth a try. ...
written 1 day ago by jean.elbers1.1k
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Answer: C: maker installation error
... the `maker` binary needs to be in your path, it is typically found in `/install-directory/bin/maker` ...
written 1 day ago by jean.elbers1.1k
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Comment: C: Can I use SNPs to date divergence?
... This is not a BEAST question but rather a SNP/coverage question I pose. Do you have enough sequencing coverage across the targets for all samples to accurately call the consensus on the sequence for each sample that you propose to input as an alignment to BEAST? For example if you have a 1000-bp tar ...
written 6 days ago by jean.elbers1.1k
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Comment: C: Contig name difference due to reference genome
... I think the biostar community needs more information to your post to help you, such as how the VCF files were produced. If the only difference is in naming, then a quick regular expression or search and replace command can replace the column 1 value from an old, undesired name to a new, desired name ...
written 11 days ago by jean.elbers1.1k
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Comment: C: Contig name difference due to reference genome
... A quick Google-search yielded: `felCat9.fa` (UCSC Genome Browser) and `GCF_000181335.3_Felis_catus_9.0_genomic.fa` (NCBI) ...
written 11 days ago by jean.elbers1.1k
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Comment: C: Getting error with awk when using parallel processing in bedtools
... I found using `GNU parallel` and `awk` tricky because of having to escape quotes and such. How many cores do you have on your computer? If it is only two, then I would just go with a non-parallel `bash` `for` loop. ...
written 22 days ago by jean.elbers1.1k
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Comment: C: repeatmasker species setting
... I don't have experience with RepeatScout, but RepeatModeler combines the output of RepeatScout and RECON (http://www.repeatmasker.org/RepeatModeler/). I personally haven't fed a custom library from RepeatModeler to RepeatMasker, but others on biostars can probably chime in ...
written 6 weeks ago by jean.elbers1.1k
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Comment: C: repeatmasker species setting
... You can also create a custom library with RepeatModeler (there are biostars posts that you can search for to get instructions) and run that model on your cephalpod genome with RepeatMasker. ...
written 6 weeks ago by jean.elbers1.1k
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Comment: C: Difference between 'raw reads' and 'spots' in PacBio and SRA
... Well perhaps it still has to do with reads passing filter...not sure ...
written 6 weeks ago by jean.elbers1.1k

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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 11 weeks ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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