Moderator: jrj.healey
jrj.healey ♦ 7.7k
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- Website:
- http://www2.warwick.ac...
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- JRJHealey
- Last seen:
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- Joined:
- 3 years, 1 month ago
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Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...
Posts by jrj.healey
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... On most Linux distributions, if you make a `bin` directory under `~`, it will be automatically added to PATH for you ;) ...
written 9 hours ago by
jrj.healey ♦ 7.7k
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... You shouldn’t need root to use make. ...
written 11 hours ago by
jrj.healey ♦ 7.7k
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... Alternatively, you may consider installing GVL or BioLinux as your base install image, which comes with a significant amount of software preconfigured. ...
written 12 hours ago by
jrj.healey ♦ 7.7k
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... Between conda, docker and brew, you can install pretty much everything without root permissions. ...
written 12 hours ago by
jrj.healey ♦ 7.7k
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... If you’re not looking to close the assemblies, and the contigs pass reasonable quality control, you can just leave them.
Alternatively, scaffold your contigs so that your small contigs are at least positioned within a final large contiguous assembly. You won’t gain more information, but you’ll make ...
written 23 hours ago by
jrj.healey ♦ 7.7k
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... Please clarify your question, it is not coherent enough for us to provide much help at this point. ...
written 1 day ago by
jrj.healey ♦ 7.7k
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... This doesn’t seem like a good idea to me because you’ll be introducing variants from different assemblies. You’ll be losing information in some areas and adding erroneous information in others. ...
written 1 day ago by
jrj.healey ♦ 7.7k
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... Try some of these perhaps?
https://omictools.com/assembly-reconciliation-category
I can’t personally speak to any of them as I’ve never tried what you’re attempting. ...
written 1 day ago by
jrj.healey ♦ 7.7k
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... Yep, Damiens answer was where I was headed. Just concatenate all you R1s and all your R2s and assemble that.
Depending on the quality, you may not want to use all of them. If you have some which are lower quality, there’s no point ‘tainting’ your other reads with them.
88 lots of fastqs may also l ...
written 1 day ago by
jrj.healey ♦ 7.7k
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... Then use a proper gene finding tools such as GeneMark or Glimmer.
Writing a python script to identify which ORFs are legitimate genes is not going to be simple.
Alternatively, use an annotation pipeline like PGAP/PROKKA, and then use biopython to count the number of `gene` or `CDS` tags that are d ...
written 1 day ago by
jrj.healey ♦ 7.7k
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