User: erwan.scaon

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erwan.scaon270
Reputation:
270
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Trusted
Location:
Limoges - CBRS
Website:
http://www.unilim.fr/r...
Last seen:
7 hours ago
Joined:
5 years, 7 months ago
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e**********@gmail.com

Posts by erwan.scaon

<prev • 24 results • page 1 of 3 • next >
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Answer: A: Discrepancy between abundance.tsv and tx2gene.csv
... If you want to convert ENSMUST00000103493.2 -> ENSMUST00000103493 in your Kallisto abundance.tsv files, you can do the following : for f in *.tsv; do awk -F '\t' -v OFS='\t' 'NR > 1 {sub(/\.[0-9]*/, "", $1)} 1' $f > ${f%%.*}"_renamed.tsv"; done; ...
written 1 day ago by erwan.scaon270
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Answer: A: Tools for Copy Number Variation analysis from ion Proton data.
... You could try : https://git.unilim.fr/merilp02/CovCop > Cov’Cop is an interactive software allowing to detect CNV from > amplicon sequencing data without reference samples. And it has been tested on Ion Proton data. ...
written 3 days ago by erwan.scaon270
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Comment: C: local blastn against one subgroup of species
... Restricting the blast search using a list of ids is a good way to go. I suggest using -seqidlist instead of -gilist, since ncbi is not going to maintain G.I. as primary identifiers for sequence records. Ps : seqidlist is a list of accession.version. How to generate the needed seqidlist list is uncl ...
written 11 days ago by erwan.scaon270
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Comment: C: Trying to match Accession numbers to Taxonomy IDs
... Ok, it seems to be a clever suggestion once again. Thanks ! (I lack a bit of knowledge on how ncbi data are organized / how to query them efficiently) ...
written 15 days ago by erwan.scaon270
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Comment: C: Trying to match Accession numbers to Taxonomy IDs
... The last hurdle : My protein database was downloaded from ncbi ftp : $ wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plant/*.protein.faa.gz &>> wget.verbose; $ cat *faa.gz > plant_refseq.faa.gz; Then, I launch a blastx against this plant_refseq database. When i query all ...
written 15 days ago by erwan.scaon270
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Comment: C: Trying to match Accession numbers to Taxonomy IDs
... Ok, I should be able to handle it from there, thanks for the tips : time zgrep -f list_5.txt \ prot.accession2taxid.gz \ | awk '{print $2"\t"$3}' $_ XP_001778611.1 3218 NP_001149654.2 4577 XP_006409976.1 72664 XP_014499952.1 3916 XP_016732373.1 3635 real 1m3 ...
written 17 days ago by erwan.scaon270
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Comment: C: Trying to match Accession numbers to Taxonomy IDs
... That seems clever, I'll try it this afternoon ...
written 17 days ago by erwan.scaon270
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Comment: C: Trying to match Accession numbers to Taxonomy IDs
... Dear community, I don't think the following question deserve a new post, given that it's largely inspired from Sej Modha answer, thus I am commenting on his answer : Question title : "Retrieving blast staxids from saccver with ncbi E-utilities" I am parsing blast+ output (custom outfmt 6 with sa ...
written 17 days ago by erwan.scaon270
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Answer: A: Trying to match Accession numbers to Taxonomy IDs
... This may be a starting point for you : Using efetch + xtract (I guess you can call it inside your javascript code ?) An example with this *Pinus taeda* nucleotide sequence : https://www.ncbi.nlm.nih.gov/nuccore/FJ070571 an='FJ070571'; efetch -db nuccore \ -id $an \ -f ...
written 5 weeks ago by erwan.scaon270
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Comment: C: Visualize Strand-Specific Rna-Seq : How To Differentiate Strands
... Very interested here too ! Did someone make any progress on this question ? ...
written 8 weeks ago by erwan.scaon270

Latest awards to erwan.scaon

Scholar 14 hours ago, created an answer that has been accepted. For A: Discrepancy between abundance.tsv and tx2gene.csv
Popular Question 3 months ago, created a question with more than 1,000 views. For COSMIC vcf file compatibility for Mutect2
Student 4 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Appreciated 7 months ago, created a post with more than 5 votes. For A: COSMIC vcf file compatibility for Mutect2
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: COSMIC vcf file compatibility for Mutect2
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
Student 9 months ago, asked a question with at least 3 up-votes. For COSMIC vcf file compatibility for Mutect2
Supporter 3.9 years ago, voted at least 25 times.
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Existing Tools For Building A De Bruijn Graph From Raw Reads
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