User: venura

gravatar for venura
venura10
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1 day, 17 hours ago
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6 months ago
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v*****@agri.pdn.ac.lk

Posts by venura

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Fetching a representative genome, gene and protein IDs from NCBI using a list o
... Sweet! Worked like a charm! Thank you @vkkodali ...
written 2 days ago by venura10
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Comment: C: Fetching a representative genome, gene and protein IDs from NCBI using a list o
... Appreciate it! Thank you! I went forward and used the extracted assemblies using the following command. cat assembly.txt | while read line; do esearch -db assembly -query "${line}" | esummary | xtract -pattern DocumentSummary -element FtpPath_RefSeq | xargs -n 1 sh -c 'wget -r -nd --no-parent - ...
written 2 days ago by venura10
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Comment: C: Fetching a representative genome, gene and protein IDs from NCBI using a list o
... Thank you @ genomax and @vkkodali cat virus.txt | while read line; do grep ${line} assembly_summary_refseq.txt >> resultfile.txt ; done Where I have the following viruses inside virus.txt > Allpahuayo mammarenavirus > Argentinian mammarenavirus > Bear Canyon mamma ...
written 2 days ago by venura10
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Comment: C: Fetching a representative genome, gene and protein IDs from NCBI using a list o
... Thank you. very helpful! Now I can retrieve assembly IDs using the method you suggested. How can I use the assembly ID to obtain all gene IDs , protein IDs, and locustags included under each assembly ID ? I will be using 200 viral genome assemblies as a query. ...
written 2 days ago by venura10
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Fetching a representative genome, gene and protein IDs from NCBI using a list of spp names
... Hi, I would like to bulk retrieve the following information for a list of virus species from NCBI. - Representative genome (e.g Machupo mammarenavirus) - Link to the genome (https://www.ncbi.nlm.nih.gov/genome/?term=Machupo+mammarenavirus) - replicon info ( Type Name RefSeq INSDC Siz ...
ncbi gene protein written 2 days ago by venura10 • updated 2 days ago by vkkodali1.8k
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Comment: C: Bulk Retrieval of Gene Sequences using Protein IDs (NCBI)
... It worked ! Thanks to both of you ! I used the following and obtained both protein and nucleotide sequences. cat nucleocapsid_clean.txt | while read line; do efetch -db protein -id ${line} -format fasta_cds_na >> resultfile ; done ...
written 7 weeks ago by venura10
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Comment: C: Bulk Retrieval of Gene Sequences using Protein IDs (NCBI)
... No! Not a Single one! I even used tamu.edu proxy. Still getting the same error. ...
written 7 weeks ago by venura10
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Comment: C: Bulk Retrieval of Gene Sequences using Protein IDs (NCBI)
... Yes I used hers. The command you gave me is working without any errors for a single ID. Please see below YP_009507925 AGE13900 YP_009505327 YP_006468898 ...
written 7 weeks ago by venura10
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Comment: C: Bulk Retrieval of Gene Sequences using Protein IDs (NCBI)
... Thank you so much for the quick reply! However, I am getting the following error; 400 Bad Request No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/e&rettype=fasta&retmode=text&edirect=7.40&tool=edirect&email=venura@felis' Result of do_post http ...
written 7 weeks ago by venura10 • updated 7 weeks ago by genomax80k
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Comment: C: Bulk Retrieval of Gene Sequences using Protein IDs (NCBI)
... Thank you so much! 🙏 Quick question, How can I add multiple query IDs into a single command? ...
written 7 weeks ago by venura10

Latest awards to venura

Scholar 5 months ago, created an answer that has been accepted. For A: MCScanx is giving an Empty Output (even for example files)

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