User: erwan.scaon

gravatar for erwan.scaon
erwan.scaon580
Reputation:
580
Status:
Trusted
Location:
Limoges - CBRS - France
Website:
http://www.unilim.fr/r...
Last seen:
1 week ago
Joined:
6 years, 8 months ago
Email:
e**********@gmail.com

Posts by erwan.scaon

<prev • 90 results • page 1 of 9 • next >
0
votes
2
answers
203
views
2
answers
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 26 days ago by erwan.scaon580
0
votes
0
answers
132
views
0
answers
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 4 weeks ago by erwan.scaon580
0
votes
0
answers
219
views
0
answers
Comment: C: strandness of paired-end data
... See also : [https://www.biostars.org/p/285757][1] [1]: https://www.biostars.org/p/285757 ...
written 8 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
Comment: C: edirect esearch : exclude given accessions
... Yes, I am using the right taxid with the cmd below, which is returning `590` taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ -element TaxId); Regarding ...
written 8 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
Comment: C: edirect esearch : exclude given accessions
... Yes, I get what you mean. I just wanted to achieve my goal (retrieve all full length genome sequences of genus Salmonella in NCBI DBs) and understand how to do it best. ...
written 11 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
Answer: A: edirect esearch : exclude given accessions
... So, here we are : I want to retrieve all full length genome sequences of genus *Salmonella*. Get *Salmonella* taxid : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ ...
written 11 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
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 11 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
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 11 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
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 11 weeks ago by erwan.scaon580
0
votes
2
answers
309
views
2
answers
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 11 weeks ago by erwan.scaon580

Latest awards to erwan.scaon

Good Question 15 days ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 3 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 4 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 6 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Teacher 8 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 8 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 8 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 10 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 11 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Teacher 11 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 11 months ago, created a question with more than 1,000 views. For Quality control for Ion Torrent
Appreciated 12 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Student 12 months ago, asked a question with at least 3 up-votes. For Retrieve genbank viral genomes
Scholar 13 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 16 months ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 17 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 20 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2
Teacher 22 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 22 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Supporter 4.9 years ago, voted at least 25 times.
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Autobiographer 4.9 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1645 users visited in the last hour