Comments (2)
Microbiology
commented on August 23, 2024
Still having memory issues on this. One answer would be to increase the threshold to 2500bp from 1000bp in an effort to reduce the amount of data being used. Should be fine anyways since these are bacterial genomes which are pretty large.
from hannigan_crcvirome_mbio_2018.
Microbiology
commented on August 23, 2024
Increasing the threshold to 2500bp worked well.
As I move forward I am going to have to be careful that I filter out those that were not part of the clustering algorithm.
from hannigan_crcvirome_mbio_2018.
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
- 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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