Comments (9)
Microbiology
commented on August 23, 2024
Okay wrote out the first script to try getting the 16S processed. I doubt it will work on the first go, but I can debug it from here.
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Microbiology
commented on August 23, 2024
Okay its going. Let's hope it holds together!
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Microbiology
commented on August 23, 2024
The process ended up dying so I think I am going to have to fix the file names to avoid special characters.
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Microbiology
commented on August 23, 2024
Okay working up to the reference database. I need to fix the link to that. Silva and whatnot.
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Microbiology
commented on August 23, 2024
Things are working with just a couple of test samples. Now Im trying to run the whole thing.
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Microbiology
commented on August 23, 2024
I'm getting hung up on the mock community stuff, which should just be a matter of fixing the names. So still a work in progress.
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Microbiology
commented on August 23, 2024
Initial processing is solid. Running the pre clustering stuff now. Fingers crossed.
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Microbiology
commented on August 23, 2024
Preclustering passed!
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Microbiology
commented on August 23, 2024
For now it looks like this part of the analysis is done. On to the next thing.
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Related Issues (20)
- Create predictive model using 16S Zackular data. HOT 2
- Cluster ORFs into OPFs HOT 2
- Calculate OPF abundance per sample. HOT 4
- Add information for sequencing depth of each of the samples. HOT 2
- Beta diversity between cancer states. HOT 2
- Add python module to CONCOCT. HOT 1
- Fix bacteria IDs to be same as sample IDs. HOT 1
- Rerun contig abundance with both virome and whole meta genome. HOT 2
- Rerun contig clustering with whole meta genome samples as well as virome. HOT 2
- Fix contig fasta problem with wrapped sequence ids. HOT 2
- Rerun files impacted by contig cat error. HOT 3
- Abundance length correction. HOT 2
- Benchmark n50, contig length distribution, alignment rate. HOT 4
- Classify contigs by blasting only the longest reads (rep sequences). Avoid short because they are less informative. HOT 5
- Fix rarefaction of samples going into random forest HOT 2
- Evaluate impact of sequencing depth on model performance. HOT 4
- Plot changes in degree centrality of fusobacterium OTU over time. HOT 1
- Create plot of lysogenic states over cancer progression. HOT 1
- Change repo name HOT 1
- Confirm that use of BLAST's `-max_target_seqs` is intentional HOT 1
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