User: Roman Luštrik

Reputation:
90
Status:
Trusted
Location:
Ljubljana, Slovenia
Twitter:
romunov
Last seen:
2 months, 3 weeks ago
Joined:
3 years, 5 months ago
Email:
r******@gmail.com

Posts by Roman Luštrik

<prev • 16 results • page 1 of 2 • next >
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Comment: C: OBITools installation error (mac OS X)
... If you're not against dockers, I've made a dockerized version of the tool, which abstracts away the arduous install process. https://hub.docker.com/r/romunov/obitools ...
written 11 months ago by Roman Luštrik90
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Answer: A: install obitools error
... If you are not averse to running a tool from docker, containerized obitools is now available (I'm the author of the repository): https://hub.docker.com/r/romunov/obitools You can use Python to send it commands, or just regular `docker exec ...`. ...
written 11 months ago by Roman Luštrik90
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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 months ago by Roman Luštrik90
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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 16 months ago by Roman Luštrik90
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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 16 months ago by Roman Luštrik90
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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 16 months ago by Roman Luštrik90
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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 16 months ago by Roman Luštrik90
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Comment: C: edger differential expression analysis error
... Can you include which warnings have been issued? ...
written 16 months ago by Roman Luštrik90
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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 3.0 years ago by Roman Luštrik90
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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 3.0 years ago by Roman Luštrik90

Latest awards to Roman Luštrik

Scholar 3.0 years ago, created an answer that has been accepted. For A: how to run obisplit in parallel
Teacher 3.4 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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