User: Janne.Swaegers

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Posts by Janne.Swaegers

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Comment: A: Threshold to exclude samples based on sample-to-sample distances
... Hi Tobias, Have you ever figured out an answer to your problem? I'm wondering about this as well... Best, Janne ...
written 2.6 years ago by Janne.Swaegers0
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Restricting ncbi nr database: from accession numbers to database. Problem with blastdbcmd: strange fasta headers and incomplete output
... Hi everyone, I want to make a blast database of insect proteins to locally blast my transcriptome assembly. I dowloaded all the accession numbers associated with insects from the ncbi website. Next, I used this command to retrieve the associated fasta files from my locally installed nr ncbi databas ...
accession number ncbi nr blast blastdbcmd written 2.6 years ago by Janne.Swaegers0 • updated 2.6 years ago by blanca10
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Comment: C: Cannot download gi list from NCBI protein
... Thanks for the link, yet downloading the accession list file from ncbi seems not be working for me (too big file?). Is there a way to circumvent this? It seems the solution is here: ftp://ftp.ncbi.nih.gov/pub/taxonomy. Yet given my limited bioinformatic knowledge the readme files are not very clear ...
written 2.7 years ago by Janne.Swaegers0
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Comment: C: Cannot download gi list from NCBI protein
... I seem to have the same problem that I cannot download the accession numbers of a large taxonomic group (in my case Insecta). Could you give more details on how to accomplish this using these listed files? Are all accession numbers available here, and how do I retrieve them for my taxonomic group of ...
written 2.7 years ago by Janne.Swaegers0

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