SchlossLab Hannigan_CRCVirome_mBio_2018 issues

SchlossLab / Hannigan_CRCVirome_mBio_2018

Investigating the gut virus communities associated with colon cancer.

MIT License

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issues

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Minor fix on line 09

#55 kant opened 3 years ago
0
Confirm that use of BLAST's `-max_target_seqs` is intentional

#54 armish closed 5 years ago
1
Pat's edits

#53 pschloss closed 5 years ago
0
Final editing

#52 pschloss closed 6 years ago
0
edits, thoughts...then submit 'er

#51 ecogenomix closed 7 years ago
0
Change repo name

#50 Microbiology closed 7 years ago
1
Edits

#49 pschloss closed 7 years ago
1
Create plot of lysogenic states over cancer progression.

#48 Microbiology closed 7 years ago
1
Plot changes in degree centrality of fusobacterium OTU over time.

#47 Microbiology closed 7 years ago
1
Evaluate impact of sequencing depth on model performance.

#46 Microbiology closed 7 years ago
4
Fix rarefaction of samples going into random forest

#45 Microbiology closed 7 years ago
2
Classify contigs by blasting only the longest reads (rep sequences). Avoid short because they are less informative.

#44 Microbiology closed 7 years ago
5
Benchmark n50, contig length distribution, alignment rate.

#43 Microbiology closed 7 years ago
4
Abundance length correction.

#42 Microbiology closed 7 years ago
2
Rerun files impacted by contig cat error.

#41 Microbiology closed 7 years ago
3
Fix contig fasta problem with wrapped sequence ids.

#40 Microbiology closed 7 years ago
2
Rerun contig clustering with whole meta genome samples as well as virome.

#39 Microbiology closed 7 years ago
2
Rerun contig abundance with both virome and whole meta genome.

#38 Microbiology closed 7 years ago
2
Fix bacteria IDs to be same as sample IDs.

#37 Microbiology closed 7 years ago
1
Add python module to CONCOCT.

#36 Microbiology closed 7 years ago
1
Beta diversity between cancer states.

#35 Microbiology closed 7 years ago
2
Add information for sequencing depth of each of the samples.

#34 Microbiology closed 7 years ago
2
Calculate OPF abundance per sample.

#33 Microbiology closed 7 years ago
4
Cluster ORFs into OPFs

#32 Microbiology closed 7 years ago
2
Create predictive model using 16S Zackular data.

#31 Microbiology closed 7 years ago
2
No 16S analysis for Zackular data.

#30 Microbiology closed 7 years ago
9
Add Zackular data download into workflow

#29 Microbiology closed 7 years ago
1
Download 16S samples for predictive modeling processing.

#28 Microbiology closed 7 years ago
1
Create figure for sample processing (bench top).

#27 Microbiology closed 7 years ago
1
Create figure for bioinformatics processing (I hate text on a poster).

#26 Microbiology closed 7 years ago
1
Prepare poster outline including introduction & methods.

#25 Microbiology closed 7 years ago
1
Run human decontamination (deconseq)

#24 Microbiology closed 7 years ago
8
Cluster contigs

#23 Microbiology closed 7 years ago
1
Call ORFs

#22 Microbiology closed 7 years ago
2
Assemble contigs

#21 Microbiology closed 7 years ago
2
QC: Rename files to MG format

#20 Microbiology closed 7 years ago
1
QC: Quality trim with FASTX

#19 Microbiology closed 7 years ago
1
QC: Trim adapters from reads

#18 Microbiology closed 7 years ago
3
Collect virome mapping file

#17 Microbiology closed 7 years ago
2
Setup virome library on Axiom git repo

#16 Microbiology closed 7 years ago
1
Get virome library in NAS `runs` directory

#15 Microbiology closed 7 years ago
1
Get whole meta genome sequences from the core

#14 Microbiology closed 7 years ago
5
Get virome sequences from core

#13 Microbiology closed 7 years ago
5
Update Sequencing Database

#12 Microbiology closed 7 years ago
2
Get replacement NexteraXT kit

#11 Microbiology closed 7 years ago
1
Final submission to sequencing core.

#10 Microbiology closed 7 years ago
4
Pool metagenome library

#9 Microbiology closed 7 years ago
2
Pool virome library

#8 Microbiology closed 7 years ago
0
Run metagenome library through Quant-IT

#7 Microbiology closed 8 years ago
2
Perform BioA Trace on NexteraXT Metagenome Library

#6 Microbiology closed 8 years ago
2