User: erwan.scaon

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erwan.scaon680
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Posts by erwan.scaon

<prev • 91 results • page 1 of 10 • next >
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Answer: A: choose between normalization techniques for OTU counts
... Hi, You should have a look at [GMPR][1] [1]: https://peerj.com/articles/4600.pdf ...
written 3 months ago by erwan.scaon680
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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 7 months ago by erwan.scaon680
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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 7 months ago by erwan.scaon680
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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 8 months ago by erwan.scaon680
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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=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ -element TaxId); Regarding ...
written 8 months ago by erwan.scaon680
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Comment: C: edirect esearch : exclude given accessions
... Yes, I get what you mean. I just wanted to achieve my goal (retrieve all full length genome sequences of genus Salmonella in NCBI DBs) and understand how to do it best. ...
written 9 months ago by erwan.scaon680
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Answer: A: edirect esearch : exclude given accessions
... So, here we are : I want to retrieve all full length genome sequences of genus *Salmonella*. Get *Salmonella* taxid : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ ...
written 9 months ago by erwan.scaon680
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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 9 months ago by erwan.scaon680
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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 9 months ago by erwan.scaon680
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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 9 months ago by erwan.scaon680

Latest awards to erwan.scaon

Appreciated 10 weeks ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Appreciated 4 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 6 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 9 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 11 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 12 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Teacher 14 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 14 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 14 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 17 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 17 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Teacher 17 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 17 months ago, created a question with more than 1,000 views. For Quality control for Ion Torrent
Appreciated 18 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Student 19 months ago, asked a question with at least 3 up-votes. For Retrieve genbank viral genomes
Scholar 19 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 23 months ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 24 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Student 2.4 years ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
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