User: rob_DNA

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rob_DNA0
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Posts by rob_DNA

<prev • 7 results • page 1 of 1 • next >
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Comment: C: esearch error "WebEnv value not found in search output - WebEnv1 Db value not f
... I now added the parameter "-api_key="my api key" in the search command and I exported it as variable in my shell and now I do not receive the error anymore. Thank you for your help! ...
written 28 days ago by rob_DNA0
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Comment: C: esearch error "WebEnv value not found in search output - WebEnv1 Db value not f
... Thank you for mentioning the API key I signed up and created an API key. I add the api key parameter like this: `esearch -db nucleotide -query "Abacoproeces saltuum [ORGN] AND 16S" | efetch -api_key="MY_API_KEY" -format fasta > Abacoproeces_saltuum.txt` Then however, I still get the error and tha ...
written 29 days ago by rob_DNA0
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esearch error "WebEnv value not found in search output - WebEnv1 Db value not found in fetch input" though search process continues
... Hi, I want to download 16S sequences (if available) of thousands of organisms. I use following command: ```esearch -db nucleotide -query "Abacoproeces saltuum [ORGN] AND 16S" | efetch -format fasta > Abacoproeces_saltuum.txt``` ```esearch -db nucleotide -query "Abax carinatus [ORGN] AND 16S" | ...
ncbi esearch entrez genbank written 4 weeks ago by rob_DNA0
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Comment: C: Trimming adapters with bbduk
... for anyone reading this in the future: https://emea.support.illumina.com/bulletins/2016/04/adapter-trimming-why-are-adapter-sequences-trimmed-from-only-the--ends-of-reads.html ...
written 6 months ago by rob_DNA0
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Comment: C: Downloading all COI sequences from BOLD fails
... I've contacted BOLD about the stalling behavior of the download, and this is their reply: "This issue is because of the large API request that retrieves millions of records, which our system does not handle. Please break up the search by smaller groups, such as classes." ...
written 6 months ago by rob_DNA0
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Comment: C: Downloading all COI sequences from BOLD fails
... Thank you for your reply. My ```wget``` command is based on that link of biostars you provide, but it now does not seem to work like that anymore. I will get in contact with them. ...
written 6 months ago by rob_DNA0
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Downloading all COI sequences from BOLD fails
... I have metabarcoding sequence data (COI) from bulk animal samples (including arthropoda, nematoda, annelida, mollusca) and I want to BLAST all of these sequences. I used following command to do this: ```blastn -remote -db nt -query COI_all.fasta -num_alignments 2 -out COI_blasted.txt```. However thi ...
software error next-gen written 6 months ago by rob_DNA0

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