User: Tom

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Tom20
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Posts by Tom

<prev • 63 results • page 1 of 7 • next >
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How to run PSSPred on multple sequences
... Hi all, I'm using PSSpred [link here][1] to predict secondary structures for a set of peptides. I am running the command on linux. When I run the command on a fasta file with a single sequence in it like this: perl PSSpred.pl test.fasta it works (i.e, it correctly predicts the secondary stru ...
psspred sequence peptide written 6 months ago by Tom20 • updated 6 months ago by Pierre Lindenbaum113k
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I know, it seems like this would be relatively straightforward, it's very frustrating. Unfortunately, I am not an expert in this particular area, so I don't feel like I know enough (yet) to try and find a workaround or understand exactly what's happening. ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Thank you; I emailed back the help desk to ask them why the file was being truncated (this happened whether I was at home or in work); they replied: Unfortunately, web displayed citation format is NOT a format supported by API. There is no good way to regenerate that format through fetched content ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Yes no problem, so this is my xtract.Darwin: http://www.filehosting.org/file/details/664811/xtract.Darwin and this is my tmp.xml (for GDS4925, the dataset in above example): http://www.filehosting.org/file/details/664812/tmp.xml Thanks for your help. I've also emailed back the help desk to ask t ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I appreciate it; Everything works great, until step 4, where I get no output at all, so there is no error I can paste (and I checked, tmp.xml is not empty). I emailed the NCBI help desk this question: > I have a list of GEO data set accession (e.g. GDS4925) and I want a > reference for each ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Thanks so much, I officially give up I think I'd rather do >100 references manually at this stage. Command 1 works (as in gives me the tmp.xml file); command 2 doesn't work (no output). So I re-installed e-utils: localhost:~ Aoife$ cd ~ localhost:~ Aoife$ perl -MNet::FTP -e \ '$ftp = ne ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I really appreciate it. I think there's something wrong with either my computer (just a standard mac terminal) or my connection to entrez. As you can see from the attached image [here][1], even when I type the first command, I just don't get the PMID back. Thank you for your help though, I appreciat ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Thanks, that's strange, on either a work server, or on my home mac laptop (no server); when I type: efetch -db pubmed -id 24670762 -format xml I can see XML output. When I type: efetch -db pubmed -id 24670762 -format xml | xtract It says (as expected) "No command-line arguments suppl ...
written 17 months ago by Tom20
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I really appreciate the help. Unfortunately, when I type: efetch -db pubmed -id 24670762 -format xml | xtract -pattern PubmedArticle -element MedlineCitation/PMID or efetch -db pubmed -id 24670762 -format xml | xtract -pattern PubmedArticle -element MedlineCitation/PMID -block A ...
written 17 months ago by Tom20
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Extract Bibliographic Reference from GEO dataset using EFetch?
... Hi all, I have say 100 data set names from GEO, and for each, I want to pull out a reference using Efetch. so for example, for the list: GDS5204 GDS520 GDS4925 The output should be: GDS4925 D'Souza M, Zhu X, Frisina RD. Novel approach to select genes from RMA normalized microar ...
geo ncbi efetch written 17 months ago by Tom20 • updated 17 months ago by Santosh Anand4.0k

Latest awards to Tom

Popular Question 10 months ago, created a question with more than 1,000 views. For Gene expression meta-analysis: How to correctly compile a data set.
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