User: anabaena

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anabaena0
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Posts by anabaena

<prev • 28 results • page 1 of 3 • next >
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Running neighborhood analysis to find genes
... Hey all, I'm looking at several proteins involved with each other in a cellular function and I have one main target gene and several others that seem to be associated with it. I am looking at binned assemblies and published on NCBI. I have a Biopython script that can pull the protein hits asso ...
biopython written 3 months ago by anabaena0
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Comment: C: Error when converting/translating .tsv ORFs to .faa
... Awesome! thanks you! ...
written 3 months ago by anabaena0
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Comment: C: Error when converting/translating .tsv ORFs to .faa
... ########################################################################################### sample ID: XXXX corresponds to Pangaea ID: XXXX # Included ENA Sample ID(s): XXX # Included ENA Run ID(s): XXXX ################################################################################ ...
written 3 months ago by anabaena0
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Error when converting/translating .tsv ORFs to .faa
... Hey all, I am working on a script to translate a mass amount of .tsv files containing predicted ORFs using biopython. I keep running into the error that a 'module is not callable when the modules are correctly loaded. Everything works until I enter the translation phase of the script when I r ...
translation orfs biopython pandas written 3 months ago by anabaena0 • updated 3 months ago by zorbax130
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Comment: C: Creating UBA protein data file in shell
... Awesome that worked, thanks! ...
written 4 months ago by anabaena0
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Creating UBA protein data file in shell
... Hey all, I am trying to create a concatenated .faa file for analysis from the UBA genome data set, I downloaded the tar and unpacked it and a folder 'bacteria' was created with sub-folders labeled UBA1330, etc. and in those subfolders are .faa files. What I need to do is concatenate all the protein ...
metagenomes uba protein .faa shell written 4 months ago by anabaena0 • updated 4 months ago by lieven.sterck8.2k
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Creating SQL of Raw Reads with Metadata/Environmental Data?
... Essentially I have a a large amount of read sets from across the world and along with those read sets I have a .csv of the corresponding environmental data (Location, O2, etc.). The goal is to go through and run assemblies with that data, but I need the assembly outputs to be matched with the meta ...
metadata metagenomics sql anvio written 4 months ago by anabaena0
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Comment: C: Downloading SRA data
... So I've managed to troubleshoot the problem as there was something wrong with the $HOME location so I replaced it with ~. Now I get the following error: > ascp: Failed to open TCP connection for SSH, exiting. > > Session Stop (Error: Failed to open TCP connection for SSH) Is this an is ...
written 4 months ago by anabaena0
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Comment: C: Downloading SRA data
... So i followed your code exactly, the only different I can think of is I have the download.txt in my scratch folder (where I have alot of download space on the HPC and not my home directory. ...
written 4 months ago by anabaena0
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Comment: C: Downloading SRA data
... I actually managed to fix that issue, now when iterating over the download files i recieve the following error > Session Stop (Error: Private key file not found at path /global/home/users/user_name/.ssh/$HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh and path /global/home/users/user_name/.ss ...
written 4 months ago by anabaena0

Latest awards to anabaena

Supporter 4 months ago, voted at least 25 times.
Scholar 6 months ago, created an answer that has been accepted. For A: assembly id from protein accession via entrez?

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