User: erwan.scaon

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erwan.scaon690
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Nantes - France
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Posts by erwan.scaon

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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 9 months ago by erwan.scaon690
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Comment: C: edirect esearch : exclude given accessions
... This returned 9 FASTA files for me, for a total of 15 sequences. My prokaryotes.txt file as 36129 lines. Did I miss something ? Edit : First download of "prokaryotes.txt" did break somehow, thus the weird results. ...
written 9 months ago by erwan.scaon690
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Comment: C: edirect esearch : exclude given accessions
... Any idea why this one "[AM933172][1]" is not returned with your command (despite being a GenBank accession) ? [1]: https://www.ncbi.nlm.nih.gov/nuccore/AM933172.1/ ...
written 9 months ago by erwan.scaon690
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Comment: C: edirect esearch : exclude given accessions
... I'll stop chatting with myself after this comment, but here is my final "dirty" solution : After checking for additional "duplicates", I found that NC_XXXXX sequences are derived from an identical sequence entry in the DB (thus need to be removed). Also found that "complete chromosome" is an acc ...
written 9 months ago by erwan.scaon690
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Comment: C: Edirect esearch exclude given accessions
... Ok, based on NZ_XX[0-9]* sequences IDs I have when downloading the non-filtered database, I came to this "dirty" solution : esearch -db nucleotide \ -query "salmonella[organism] \ AND complete genome[Title] \ NOT contig[Title] \ ...
written 9 months ago by erwan.scaon690
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edirect esearch : exclude given accessions
... Dear all, I am trying to retrieve all *Salmonella* complete genomes from NCBI nucleotide DB (without redundancy). This is my current try : esearch -db nucleotide \ -query "salmonella[organism] \ AND complete genome[Title] \ NOT contig[Title] ...
ncbi edirect esearch written 9 months ago by erwan.scaon690
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Comment: C: Number of mapped reads from BAM file
... Dear Ryan, I wanted to apply your logic for counting uniquely mapped reads within paired-end datasets (STAR). My goal is, for a given location, to count the number of reads on forward and reverse strand (also using advices given [here][1]). First, if I disregard the fact that my dataset is paired ...
written 10 months ago by erwan.scaon690
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Answer: A: Fasta file filtering
... You can easily achieve this with [seqtk][1]. Quoting from the manual : > Extract sequences with names in file name.lst, one sequence name per line: > seqtk subseq in.fq/fa name.lst > out.fq/fa [1]: https://github.com/lh3/seqtk ...
written 13 months ago by erwan.scaon690
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Comment: C: Parsing Blast output on linux/unix
... If you don't have to stick to XML, you should try tabular output (outfmt 6). Then you can start learning how to parse it from [ncbi webinar][1]. Basic UNIX command lines will work far better on tabular output compared to XML. [1]: https://www.youtube.com/watch?v=BIBL-wYhAl4 ...
written 13 months ago by erwan.scaon690
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Comment: C: Kallisto TPM values
... You should post or link your question on the [google_group][1]. You may also find an answer to your question from previous posts on this google_group. Does [this one][2] help ? [1]: https://groups.google.com/forum/#!forum/kallisto-sleuth-users [2]: https://groups.google.com/forum/#!searchin/k ...
written 13 months ago by erwan.scaon690

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Appreciated 3 months ago, created a post with more than 5 votes. For A: 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 Question 5 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 7 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
Popular Question 10 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
Popular Question 13 months ago, created a question with more than 1,000 views. For Read pair orientation : Illumina TruSeq Stranded mRNA library
Teacher 15 months 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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Scholar 15 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 18 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Scholar 18 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Teacher 18 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 18 months ago, created a question with more than 1,000 views. For Quality control for Ion Torrent
Appreciated 19 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 20 months ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 24 months ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 2.1 years ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2
Teacher 2.4 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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