User: Roman Valls Guimerà

Reputation:
530
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Trusted
Location:
Melbourne
Website:
https://blogs.nopcode....
Twitter:
@braincode
Last seen:
5 months ago
Joined:
10 years, 2 months ago
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b*********@nopcode.org

Posts by Roman Valls Guimerà

<prev • 58 results • page 1 of 6 • next >
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Answer: A: Where Can I Download Some Bam Files?
... Some here too: https://github.com/brainstorm/tiny-test-data ...
written 5 months ago by Roman Valls Guimerà530
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Comment: C: Tool for random access to indexed BAM files in S3?
... See: https://www.biostars.org/p/385688/#385818 ...
written 11 months ago by Roman Valls Guimerà530
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Comment: C: Using samtools to view an indexed file in a private S3 bucket
... Also, make sure you keep the AWSAccessKeyId, signature, etc... parameters after the '?' on your `samtools view` command, otherwise the (presigned) URL will not be accessible. ...
written 11 months ago by Roman Valls Guimerà530
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Job: RSE and Bioinformatics positions for the University of Melbourne for Cancer Research
... Please follow this link and apply!: https://twitter.com/fiamh/status/1128462516177129472 ...
bioinformatics rse job written 12 months ago by Roman Valls Guimerà530
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News: Integrative Genomic Viewer (IGV) works with Amazon S3
... Still on its way to get accepted upstream, but it works well for us so far: https://blog.umccr.org/2019/02/16/igv-amazon/ Hope it helps! ...
news amazon igv written 15 months ago by Roman Valls Guimerà530
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Answer: A: Where Can I Download Some Bam Files?
... For a quick-gratification one-liner (instead of multi-step and multi-MB approaches), one could just use that command (after installing samtools): samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17 ...
written 19 months ago by Roman Valls Guimerà530
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... The table is outdated by now, Snakemake does support Kubernetes AFAICT: https://snakemake.readthedocs.io/en/stable/executable.html#executing-a-snakemake-workflow-via-kubernetes ...
written 2.1 years ago by Roman Valls Guimerà530
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Answer: A: Is There An Easy Way Of Getting Gene Symbols From Genomic Coordinates?
... In today's (2018) `cruzdb` it seems to require a bit more work than that since one has to iterate/fetchall through the sql query (also give the intervals with integers instead of `str`): In [9]: from cruzdb import Genome ...: hg18 = Genome('hg18') ...: hg18.bin_query('refGene', 'chr1' ...
written 2.1 years ago by Roman Valls Guimerà530
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Is there a standalone VCF file anonymizer tool?
... While tracking down a bug by yet another VCF parsing/filtering script, I realized that trimming a VCF is quite tedious and prone to shaving the actual bug while doing so while preparing the test case. Does anybody know of a VCF randomizer/anonymizer/fuzzer that would allow me to share (cancer) sens ...
vcf written 3.0 years ago by Roman Valls Guimerà530
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Answer: A: TCGA tumor/normal RNA-seq somatic mutation calling
... Perhaps you can give a try to [this one][1]? [1]: https://bcbio-nextgen.readthedocs.org/en/latest/contents/pipelines.html#cancer-variant-calling ...
written 4.3 years ago by Roman Valls Guimerà530 • updated 20 months ago by RamRS27k

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Good Answer 3.0 years ago, created an answer that was upvoted at least 5 times. For A: Distributed Computing In Bioinformatics
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Inter
Epic Question 4.6 years ago, created a question with more than 10,000 views. For Generating .Vcf.Idx Files From Cmdline
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Good Question 5.6 years ago, asked a question that was upvoted at least 5 times. For Faster Illumina Analysis Pipeline Via Streaming
Appreciated 5.6 years ago, created a post with more than 5 votes. For C: Cloud Computing Real Implication On Bioinformatics
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Generating .Vcf.Idx Files From Cmdline
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Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Distributed Computing In Bioinformatics
Student 8.4 years ago, asked a question with at least 3 up-votes. For Faster Illumina Analysis Pipeline Via Streaming
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Teacher 8.5 years ago, created an answer with at least 3 up-votes. For A: Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Inter
Popular Question 8.5 years ago, created a question with more than 1,000 views. For Generating .Vcf.Idx Files From Cmdline
Teacher 8.9 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Popular Question 9.1 years ago, created a question with more than 1,000 views. For Sample Identifier Standard For Lims Systems ?
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