User: erwan.scaon

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erwan.scaon790
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Posts by erwan.scaon

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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 20 months ago by erwan.scaon790
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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 21 months ago by erwan.scaon790
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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 23 months ago by erwan.scaon790

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Good Question 16 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
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For Retrieve genbank viral genomes
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Scholar 2.5 years ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 2.8 years ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
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