User: Roman Luštrik

Reputation:
70
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Trusted
Location:
Ljubljana, Slovenia
Twitter:
romunov
Last seen:
6 days, 20 hours ago
Joined:
2 years, 4 months ago
Email:
r******@gmail.com

Posts by Roman Luštrik

<prev • 14 results • page 1 of 2 • next >
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Answer: A: How to call BBMap, SAMTools and GATK from Python or Ruby?
... You can run it using package `plumbum`. from plumbum import local samtools = local['samtools'] # or relative/absolute path to samtools print(samtools['--help']()) Output: Program: samtools (Tools for alignments in the SAM format) Version: 1.8 (using htslib 1.8) Usage ...
written 12 days ago by Roman Luštrik70
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Answer: A: Difference between primary nad capture targets
... I have struggled with this recently and am still lamenting why things are not standardized, at least terminology-wize. @Wouter has already explained well what is going on. I would just like to add, if I'm not mistaking (correct me if I am), that: A bed file which holds the wishlist (based on a geno ...
written 3 months ago by Roman Luštrik70
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Comment: C: bait interval list for picard collecthsmetrices
... Can you cite any references about this? I noticed that terminology regarding regions, targets, baits, "covered" regions... has much room for improvement between kit and tool providers. I think [BaitDesigner](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_util_BaitDes ...
written 3 months ago by Roman Luštrik70
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Comment: C: Variant calling with GATK on human cancer samples aligned against GRCh38.p10
... How would one reconcile UCSC/ENSEMBL difference in annotation for this file? E.g. hg38 has chromosomes named "chr1" while GRCh38 has "1". There are probably differences in other contigs as well? ...
written 3 months ago by Roman Luštrik70
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Comment: C: Variant calling with GATK on human cancer samples aligned against GRCh38.p10
... Has anyone managed to find a GRCh38 version of 1000G and Hills & 1000G indels? ...
written 3 months ago by Roman Luštrik70
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Comment: C: edger differential expression analysis error
... Can you include which warnings have been issued? ...
written 3 months ago by Roman Luštrik70
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Answer: A: how to run obisplit in parallel
... The solution was more obvious than initially thought. I was referencing the wrong .fastq file and the output of `obisplit` was for some reason on that particular file, printed to output. When I switched to the right file, everything folded into place. ...
written 2.0 years ago by Roman Luštrik70
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Comment: C: how to run obisplit in parallel
... I have tried various ways of what you've suggested but still no dice. What I care about is that file must have the right designation as assigned by obisplit (e.g. `DATA_processed_color_bookeeping_*red*`), the rest is just bookkeeping which I can handle later on. ...
written 2.0 years ago by Roman Luštrik70
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how to run obisplit in parallel
... `obitools`'s [`obisplit` command](http://metabarcoding.org/obitools/doc/scripts/obisplit.html) will take a file of sequences and sort reads into separate files, which it will name according to some specified attribute of sequences. The command obisplit -p DATA_ -t color input.fastq will result ...
obisplit fastq parallel obitools linux written 2.0 years ago by Roman Luštrik70
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Comment: C: how to split/cut/restrict DNA strand
... Thank you @WouterDeCoster. I may end up using this in another part of the pipeline. ...
written 2.3 years ago by Roman Luštrik70

Latest awards to Roman Luštrik

Scholar 2.0 years ago, created an answer that has been accepted. For A: how to run obisplit in parallel
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: how to add lines to a plot gradually (ggplot2) ?

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