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GenoMax
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Recent Replies
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…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
•
0
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
by
Ram
43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2
by
Ram
43k
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
by
Pierre Lindenbaum
161k
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
by
GenoMax
141k
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.…
Comment: Per base sequence content failed miserably
by
GenoMax
141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ?
by
kjngo
•
0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Answer: Downloaded pdb's on rcsb.org
by
GenoMax
141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services
It could be as …
Answer: How to compare the quality of assemblies
by
shelkmike
★
1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴
300
Thank you very much for your answer, that was very helpful!
> Impossible to say. It depends on your data, particularly on how the donors …
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