User: erwan.scaon

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erwan.scaon750
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Nantes - France
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Posts by erwan.scaon

<prev • 93 results • page 1 of 10 • next >
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Answer: A: Algorithm based differences between Mutect2 and Haplotypecaller?
... Some good reads : [link1][1], [link2][2] [1]: https://gatkforums.broadinstitute.org/gatk/discussion/8146/some-questions-about-difference-between-haplotypecaller-and-mutect2 [2]: https://software.broadinstitute.org/gatk/documentation/article?id=11127 ...
written 6 months ago by erwan.scaon750
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Answer: A: Genome assembly statistical tools
... You should have a look at [SQUAT][1] [1]: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5445-3 ...
written 6 months ago by erwan.scaon750
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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 11 months ago by erwan.scaon750
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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 15 months ago by erwan.scaon750
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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 15 months ago by erwan.scaon750
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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 16 months ago by erwan.scaon750
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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=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ -element TaxId); Regarding ...
written 16 months ago by erwan.scaon750
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Comment: C: edirect esearch : exclude given accessions
... Yes, I get what you mean. I just wanted to achieve my goal (retrieve all full length genome sequences of genus Salmonella in NCBI DBs) and understand how to do it best. ...
written 17 months ago by erwan.scaon750
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Answer: A: edirect esearch : exclude given accessions
... So, here we are : I want to retrieve all full length genome sequences of genus *Salmonella*. Get *Salmonella* taxid : taxid=$(esearch -db taxonomy \ -query 'Salmonella' \ | efetch -format xml \ | xtract -pattern Taxon \ ...
written 17 months ago by erwan.scaon750
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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 17 months ago by erwan.scaon750

Latest awards to erwan.scaon

Popular Question 10 weeks ago, created a question with more than 1,000 views. For ChIP-Seq samples : FASTQ quality control
Great Question 6 months ago, created a question with more than 5,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Great Question 6 months ago, created a question with more than 5,000 views. For COSMIC vcf file compatibility for Mutect2
Appreciated 10 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Appreciated 13 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 14 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 17 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 19 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Popular Question 21 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
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
Teacher 23 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 23 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 2.1 years ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 2.1 years ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Quality control for Ion Torrent
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Student 2.3 years ago, asked a question with at least 3 up-votes. For Retrieve genbank viral genomes
Scholar 2.3 years ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 2.6 years ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 2.7 years ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2

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