User: erwan.scaon

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erwan.scaon210
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Location:
Limoges - CBRS
Website:
http://www.unilim.fr/r...
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5 years, 5 months ago
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Posts by erwan.scaon

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Visualize Strand-Specific Rna-Seq : How To Differentiate Strands
... Very interested here too ! Did someone make any progress on this question ? ...
written 3 days ago by erwan.scaon210
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Comment: C: Obtain full taxonomic hierarchy from multiple species names
... If you want to focus on the main taxonomic ranks, i.e. superkingdom, kingdom, phylum, class, order, family, genus & species, you can do the following : efetch -db taxonomy \ -id 9606 \ -format xml \ | xtract -pattern Taxon \ -tab '\n' -sep '\t' \ ...
written 17 days ago by erwan.scaon210
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Comment: C: STAR mapper: unrecoginzed parameter name "sjdbInsertSave" in input "genomeParame
... Ok, my bad, this "error" was due to "version conflict" : STAR genome index was built with version 2.5.2b but mapping was attempted on a different cluster with an older version. Mapping with version 2.5.2b works fine. ...
written 9 weeks ago by erwan.scaon210
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Answer: A: STAR mapper: unrecoginzed parameter name "sjdbInsertSave" in input "genomeParame
... I stumbled across the same issue (STAR, version 2.5.2b). Exactly the same error message (with the wrong spelling for unrecoginzed). Thing is, "sjdbInsertSave" is an actual parameter name, I don't get why it would be "unrecognized" all of a sudden. Any tips ? ...
written 9 weeks ago by erwan.scaon210
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Answer: A: Retrieve genbank viral genomes
... When you go to https://www.ncbi.nlm.nih.gov/genome/viruses => "Accession list of all viral genomes" => taxid10239.nbr, this is indeed a neighbours file. I think it contains a little more than 9096 entries, because some lines have multiples accession numbers : - awk -F "\t" '!/^#/ {print $1}' ...
written 3 months ago by erwan.scaon210
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Retrieve genbank viral genomes
... Hi dear community ! *Ps* : The following question was ofc googled, I came across two biostars posts (see below), but I still need some enlightenments : https://www.biostars.org/p/192391/, https://www.biostars.org/p/98218/. For a metagenomic analysis, I'd like to locally retrieve all bacterial, fun ...
genome viral ncbi genbank download written 3 months ago by erwan.scaon210
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Answer: A: COSMIC vcf file compatibility for Mutect2
... Indeed, you should use both coding and non-coding variants. In our MuTect2 project, we ended up using the hg19 COSMIC files for both coding and non-coding : # Retrive files sftp "erwan.scaon@unilim.fr"@sftp-cancer.sanger.ac.uk; get files/grch37/cosmic/v79/VCF/CosmicCodingMuts.vcf.gz get files/g ...
written 5 months ago by erwan.scaon210
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Answer: A: GATK BaseRecalibrator - Input files knownSites and reference have incompatible c
... I stumbled across something similar recently. I finally managed to get rid of the "incompatible contigs" error : https://www.biostars.org/p/232994/ ...
written 8 months ago by erwan.scaon210
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Answer: A: COSMIC vcf file compatibility for Mutect2
... Ok, things are working for me, i did the following to make my "grch38" cosmic.vcf compatible with human genome reference hg38 (downloaded from GATK bundle) : --- convert cosmic contigs names from "1" -> "chr1" awk '{if($0 !~ /^#/) print "chr"$0; else print $0}' CosmicCodingMuts.vcf > Cos ...
written 8 months ago by erwan.scaon210
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COSMIC vcf file compatibility for Mutect2
... I am running a variant calling pipeline for cancer samples. It includes Mutect2. Working on human, i started with the reference & dbsnp files contained in the GATK bundle for hg38 (ftp://ftp.broadinstitute.org/bundle/hg38). Picked the following files : Homo_sapiens_assembly38.dict Homo_sapiens ...
vcf gatk mutect2 cosmic written 8 months ago by erwan.scaon210

Latest awards to erwan.scaon

Popular Question 9 weeks ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 3 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 5 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Student 7 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Supporter 3.7 years ago, voted at least 25 times.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
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