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Recent Replies
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
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3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: Removing duplicates
by
joe
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500
I'd try those OP @samuel recommends
My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
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swbarnes2
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No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do:
bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option.
Get the PDB ID's
$ ./get.sh "Mus musculus" AHR
4M4X
5NJ8
5V0L
8H77
Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that.
EDIT: I've updated that number to 250. I'm hoping you won't need …
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script:
```bash
organism=$(echo $1 | sed 's/ /%20/g')
gene=$2
curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
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GenoMax
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This question does not make complete sense. If you have your own data files why do you need deep sequencing reads?
Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like:
https://www.rcsb.org/search?requ…
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