Moderator: lakhujanivijay
lakhujanivijay ♦ 5.3k
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Bioinformatician 💻 | ☕ Programmer
A passionate bioinformatician interested in developing solutions for analyzing, visualizing and integrating clinical and research data.
Me = ( ¼ Bioinformatician ) + ( ¼ Programmer ) + ( ½ Biologist )
Let's connect !
Find me on ORCID
https://orcid.org/0000-0002-6529-0841Posts by lakhujanivijay
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... Hi all
Before I start writing my own code to convert GTF file into a JSON format file, has anyone came across any API or tool to either convert or download the file is JSON ?
I am looking for a format like this - `gene -> transcript -> exon` :
"MOS": {
"NM_005372.1": [
...
written 5 weeks ago by
lakhujanivijay ♦ 5.3k
• updated
5 weeks ago by
vkkodali • 2.4k
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Comment:
C: how to choose hub genes in wgcna
... Hi Parin
Check out similar posts on Biostars and see if that helps
https://www.biostars.org/p/419867/
https://www.biostars.org/p/294436/
Similar posts appear on the right of the original post
...
written 12 weeks ago by
lakhujanivijay ♦ 5.3k
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... The program specific issues are hard to resolve here because many of the tools are not that popular. Best option is to raise an issue of the respective github repository. I could see similar issue reported [here][1] with no solution
[1]: https://github.com/neherlab/pan-genome-analysis/issues/36 ...
written 3 months ago by
lakhujanivijay ♦ 5.3k
0
votes
0
answers
300
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Comment:
C: Help needed with LOHHLA pipeline
... https://www.biostars.org/u/49081/ were you able to resolve the issue ? Can you check once if your BAM file is not truncated ?
\* `samtools quickcheck -v -v -v -v `
\* Requires latest samtools version ...
written 3 months ago by
lakhujanivijay ♦ 5.3k
0
votes
1
answer
242
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1
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Comment:
C: network construction in cytoscape
... Hi https://www.biostars.org/u/63328/
Can you point us to the tutorial you are following ? ...
written 3 months ago by
lakhujanivijay ♦ 5.3k
2
votes
1
answer
142
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1
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Answer:
A: phenotype in meta analysis
... Hi Parin
Quoting from [this][1] paper
> One approach to increase power for GWASs on a phenotype that is hard
> to collect is to utilize an intermediate or proxy phenotype that is
> correlated to the target phenotype of interest. In this approach, one
> intermediate or proxy phenotype, ...
written 3 months ago by
lakhujanivijay ♦ 5.3k
0
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0
answers
215
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... Hi https://www.biostars.org/u/40156/
`/WGS_tools/ChIA-PIPE/0.chia_pipe_shell.sh: line 208: pigz: command not found`
I could also see this error in your original post; were you able to resolve this?
...
written 4 months ago by
lakhujanivijay ♦ 5.3k
0
votes
0
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... Agree with what https://www.biostars.org/u/30/ said ...
written 4 months ago by
lakhujanivijay ♦ 5.3k
1
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0
answers
334
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0
answers
... **Using [GNU parallel][1] instead**
> **psuedo code**
import subprocess
cmd_file_name = cmd_file.txt
cmd_file = open(cmd_file_name, "a")
jobs = 20
for i in your_sample_list :
cmd = " ".join( [ "your command", "-i" , i ] )
cmd_file.write(cmd, "\n ...
written 4 months ago by
lakhujanivijay ♦ 5.3k
• updated
4 months ago by
_r_am ♦ 32k
0
votes
0
answers
234
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Comment:
C: hhblits and pssm
... Hi https://www.biostars.org/u/67543/
The title "hhblits and pssm" does not qualify as a good/informative title to your post. Please elaborate the title. ...
written 4 months ago by
lakhujanivijay ♦ 5.3k
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