User: erwan.scaon

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erwan.scaon630
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Location:
Limoges - CBRS - France
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http://www.unilim.fr/r...
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Posts by erwan.scaon

<prev • 90 results • page 1 of 9 • next >
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Answer: A: DESEQ2 size factors change when number of samples change in the design
... > So if you have 1 large experiment its better to put everything > together and then perform comparisons It is still true if said large experiment was done on multiple Illumina runs (compute size factor for all samples on all runs) ? Or shall we compute size factor for all samples per Illumi ...
written 3 months ago by erwan.scaon630
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Find the closest Salmonella complete genome (starting with a NGS sample from a single Salmonella strain)
... Dear all, I wish to find the closest *Salmonella* complete genome for any given input NGS sample. There are 600+ complete *Salmonella* genomes available. That makes for a "database" with a lot of very close/related sequences (strains). I already tried [StrainSeeker][1]. First test against this so ...
salmonella strainseeker snippy written 3 months ago by erwan.scaon630
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Comment: C: strandness of paired-end data
... See also : [https://www.biostars.org/p/285757][1] [1]: https://www.biostars.org/p/285757 ...
written 4 months ago by erwan.scaon630
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Comment: C: edirect esearch : exclude given accessions
... Yes, I am using the right taxid with the cmd below, which is returning `590` taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ -element TaxId); Regarding ...
written 4 months ago by erwan.scaon630
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Comment: C: edirect esearch : exclude given accessions
... Yes, I get what you mean. I just wanted to achieve my goal (retrieve all full length genome sequences of genus Salmonella in NCBI DBs) and understand how to do it best. ...
written 4 months ago by erwan.scaon630
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Answer: A: edirect esearch : exclude given accessions
... So, here we are : I want to retrieve all full length genome sequences of genus *Salmonella*. Get *Salmonella* taxid : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ ...
written 4 months ago by erwan.scaon630
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Comment: C: edirect esearch : exclude given accessions
... Ok, this "efilter -source insd" is working well ! If I compare my "dirty" solution with yours : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ -elemen ...
written 4 months ago by erwan.scaon630
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Comment: C: edirect esearch : exclude given accessions
... Did you download "prokaroytes.txt" today ? Do you mind sharing a file with full "grep -w "Complete" prokaryotes.txt | grep -w "Salmonella"" output so that we can run "comm" ? *Ps* : I am already quite confident that the previous solution yielding 420 sequences is not good enough, given that it's ...
written 4 months ago by erwan.scaon630
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Comment: C: edirect esearch : exclude given accessions
... Ubuntu 16.04 grep (GNU grep) 2.25 grep -w "Complete" prokaryotes.txt | grep -w "Salmonella" | head -2 > Salmonella enterica subsp. enterica serovar Typhi str. > CT18 220341 PRJNA236 236 Proteobacteria Gammaproteobacteria 5.13371 51.8776 chromosome:NC_003198.1/AL513382.1; > plasmid pH ...
written 4 months ago by erwan.scaon630
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Comment: C: edirect esearch : exclude given accessions
... axel -q ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/prokaryotes.txt; grep -w "Complete" prokaryotes.txt | grep -w "Salmonella" | awk 'BEGIN{FS="\t"}{print $21}' | awk 'BEGIN{OFS=FS="/"}{print "wget "$0,$NF"_genomic.fna.gz"}' | wc -l; > 458 ! ...
written 4 months ago by erwan.scaon630

Latest awards to erwan.scaon

Appreciated 25 days ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Question 25 days ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Good Question 11 weeks ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 5 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 7 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 8 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Scholar 10 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 13 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 13 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Popular Question 13 months ago, created a question with more than 1,000 views. For Quality control for Ion Torrent
Appreciated 14 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Student 14 months ago, asked a question with at least 3 up-votes. For Retrieve genbank viral genomes
Scholar 15 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 19 months ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 19 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 22 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2
Teacher 24 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 2.0 years ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
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Teacher 5.1 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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