User: sovrappensiero

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Posts by sovrappensiero

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NCBI EUtils: identifying projects with both NGS and Sanger sequencing
... I'd like to write a short script to identify BioProjects in NCBI where the researchers have done two forms of sequencing - say, NGS and confirmatory Sanger sequencing. These don't seem to show up under the index list for "Project Data Type." I looked through the XML output of some of the BioProjec ...
ncbi data type eutils written 4 weeks ago by sovrappensiero10
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... Can someone else do this on behalf of the authors? There is no link between that BioProject PRJEB31886 and their paper. However, the BioProject ID is mentioned in the paper. EDIT: I just realized that there is no XML output available for that BioProject (it says the ID 31886 is not public; I used ...
written 4 weeks ago by sovrappensiero10
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... Thanks. This is something I can work it into an automated script. It's very helpful to realize that the publication is embedded in the XML output - thank you for your answer! ...
written 4 weeks ago by sovrappensiero10
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... I also learned that NCBI discourages authors from putting their BioProject accession in their manuscript (but they can include the SRA entries). [Should I cite BioProject accession numbers in my manuscript?][1] [1]: https://www.ncbi.nlm.nih.gov/bioproject/docs/faq/#should-i-cite-bioproject-acces ...
written 4 weeks ago by sovrappensiero10
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Comment: C: Elink to get PMID associated with a BioProject or SRA entry
... I believe it is [this paper][1], with the same title as the project. I found it by searching the BioProject title in Google. But this is too cumbersome for hundreds (or even tens...) of these. EDIT: It's definitely this paper. They have mentioned the BioProject ID in the paper itself (and they i ...
written 4 weeks ago by sovrappensiero10
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Elink to get PMID associated with a BioProject or SRA entry
... Is there any way through command line EUtils to identify publication(s) associated with a particular BioProject, or from a run entered in SRA database? For example, something like this (but this doesn't work): esearch -db bioproject -query "PRJEB31886" | elink -target pubmed As far as I know, ...
ncbi bioproject eutils pmid pubmed written 4 weeks ago by sovrappensiero10 • updated 4 weeks ago by Istvan Albert ♦♦ 85k
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Comment: C: How to download oxford nanopore sequencing fast5 files from SRA
... Is there a way to do this via command line (if not using AWS)? I used SRA Toolkit to grab fastq files for Illumina sequences, but I need a few Nanopore sequences as well now. I'd like to keep doing everything from command line, but it seems I can't do it with SRA Toolkit. Wondering if there is an ...
written 5 weeks ago by sovrappensiero10
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Comment: C: Entrez Direct E-utilities on command line: efilter parameters for limiting efetc
... Ok, I understand it now. Clever! Thank you so much for the help. ...
written 12 months ago by sovrappensiero10
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Comment: C: primersearch Illegal character '/' error: EMBOSS An error in primersearch.c at
... Thanks! I had checked that. I figured out that the problem was with my primer file - basically I had two, each formatted differently for different purposes, and I was calling the wrong one. Stupid mistake. Still, that was a strange error...would been a lot easier to troubleshoot the problem if t ...
written 12 months ago by sovrappensiero10
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primersearch Illegal character '/' error: EMBOSS An error in primersearch.c at line 499
... I am trying to run primersearch to get a large batch of primer pairs against a directory of around 45 fasta files. When I try to run it for one using the command below, I get the error that follows. I also have the debug file, but I don't know how to upload that. I've tried with EMBOSS/6.5.7 and ...
warning primersearch emboss error written 12 months ago by sovrappensiero10

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