User: colindaven
colindaven • 830
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Posts by colindaven
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...
#!/bin/bash
for i in `ls *.fastq`
do
soapdenovo2 $i &
done
You'll need to set up the config files for each separately though but try that. Otherwise try something like Abyss which doesn't need a config file. ...
written 1 day ago by
colindaven • 830
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Comment:
C: ChIP-Seq for viral genomes
... I think your analysis is correct, and the tools are optimised for large genomes. Never had to do small genome chip-seq analysis, thankfully.
I think careful manual curation is appropriate in this case.
One thing that has really helped me in Chip-seq analysis is using the Mulitbamsummary tools then ...
written 1 day ago by
colindaven • 830
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Comment:
C: ChIP-Seq for viral genomes
... Not really answering your question, but I'd be concerned with cross contamination to the host (human?) genome. I would definitely do the short experiment of adding your virus genome to the human genome and then aligning all reads and redoing the MACS analysis.
I bet there are a few false positive ...
written 5 days ago by
colindaven • 830
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... Theres a tool called metassembler which might help you out.
https://github.com/biol7210-genomes/assemblers/blob/master/metassembler.md
However, it's a difficult and inherently biased undertaking. I'd try to pick the two most complete assemblies for use. I.e. #2 and #4
Actually, #2 looks pretty ...
written 6 days ago by
colindaven • 830
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... I wouldn't divide up the fastq.
Soapdenovo2 might be more memory efficient for you.
Minia certainly will be, but assemblies are poor in my experience.
Good luck.
If you're really struggling and those tools don't work I could perhaps run assemblies for you if you gave me the exact commands to run ...
written 6 days ago by
colindaven • 830
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C: Nanopore only assembly errors
... Sounds like you have done everything right. There is a lot known about P. aeruginosa and heaps of phylogeny information. If you can't do additional Illumina seq to correct the indels (that number of indels, i.e. 30% is the worst I've heard) maybe you can use public Illumina reads from an almost iden ...
written 19 days ago by
colindaven • 830
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... You can monitor the process with the following tools
- gotop
- htop
- glances
These should be easily installable under Ubuntu.
But please state your server specs !
- RAM
- hard disk space
140m PE illumina sequences will require a significant amount of mem and HDD space. I would guess at 6 ...
written 19 days ago by
colindaven • 830
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Comment:
C: Nanopore only assembly errors
... This sounds too high.
- Which genome ? Prok/Euk? Size ?
- How many rounds to nanopolish polishing ?
- Which assembler was used?
- Are the indels in reading frames? ...
written 21 days ago by
colindaven • 830
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... Nonetheless, it's a nice tool and it's great people are trying to speed up bioinformatics infrastructure akin to what is going in the commercial and semi-commercial world with DRAGEN, MPEG-G and so on. So I will test a bit on Illumina X10 and NextSeq data I have and give feedback on any bugs I encou ...
written 21 days ago by
colindaven • 830
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... You're right to be sceptical. I have spent a long time working in and around this area. In any rate, it is a lot more robust than 16S.
Nonetheless, I would always assess bacterial shotgun metagenomes with multiple tools and databases. Also, BLAST analysis can be helpful. Finally, controls are incre ...
written 22 days ago by
colindaven • 830
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