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Recent Replies
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
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Ram
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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…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
•
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Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★
1.7k
great guidance ... thank you
Comment: error in CPC2
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Ram
43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2
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Ram
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Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
Comment: python file for cpc2
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Pierre Lindenbaum
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https://academic.oup.com/nar/article/45/W1/W12/3831091
> CPC2: a fast and accurate coding potential calculator based on sequence intrinsic…
Comment: error in CPC2
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GenoMax
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Looks like you are running code that was written for `python v.2.x` but you probably have `python v.3.x` or a newer version than `python v.…
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If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
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by
kjngo
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Thanks changing the tmp dir fixed the out of disk space error for me as well.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
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Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services
It could be as …
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