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Commentator to
GenoMax
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jkbonfield
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Recent Replies
Comment: Removing duplicates
by
joe
▴
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
by
swbarnes2
14k
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
by
GenoMax
141k
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…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1
Here's the JSON from your search query:
```
{
"query": {
"type": "grou…
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