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hputnam
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Meth_Compare
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Genome feature/CpG overlap characterizations
#60
yaaminiv
closed
4 years ago
3
Add TE and flanking region information to genome feature overlap pipeline
#59
yaaminiv
closed
4 years ago
1
Statistical test for methylation frequency distribution
#58
yaaminiv
closed
4 years ago
4
Create flanking region track
#57
yaaminiv
closed
4 years ago
1
RepeatMasker TE tracks for both species
#56
yaaminiv
closed
4 years ago
0
Create 10x union bedgraphs for both species
#55
sr320
closed
4 years ago
0
Investigate MetaPlotR for genome feature/methylation figures
#54
yaaminiv
closed
4 years ago
0
Fix for Emu mess
#53
kubu4
closed
4 years ago
1
Revert repo to commit e9cf685?
#52
kubu4
closed
4 years ago
20
conversion efficiency with lambda vs est. from non CpG methylation
#51
shellywanamaker
closed
4 years ago
0
Potential for annotating exons in Mcap and Pact genomes
#50
yaaminiv
closed
4 years ago
0
Upload bismark bedgraphs, .cov, and .bam files to OSF
#49
shellywanamaker
closed
4 years ago
6
Fix Google Drive access for those external to URI
#48
hputnam
closed
4 years ago
0
Explore why different methods produce different meth outcomes for each species
#47
yaaminiv
closed
4 years ago
1
Consider idea for genome feature analysis Aberg et al 2017
#46
shellywanamaker
closed
4 years ago
1
Align Pact reads against Pact/C1 Pangenome
#45
sr320
closed
4 years ago
10
Develop a encompassing script to redo bioinformatics
#44
sr320
closed
4 years ago
1
Union bedgraphs for circos plots?
#43
shellywanamaker
closed
4 years ago
11
5x vs. 10x data?
#42
yaaminiv
closed
4 years ago
2
Add MD5 check and MultiQC to OSF?
#41
shellywanamaker
closed
4 years ago
0
Look into Liew/Li exon annotations
#40
yaaminiv
closed
4 years ago
1
Update methylation frequency distribution figure
#39
yaaminiv
closed
4 years ago
1
Rerun CpG characterization with full samples after QC
#38
yaaminiv
closed
4 years ago
3
Use MultiQC reports to generate tables in automated fashion
#37
hputnam
closed
4 years ago
11
Can you get UTR from a CDS track?
#36
yaaminiv
closed
4 years ago
1
md5 check script
#35
sr320
closed
4 years ago
9
Check Bioinformatics Markdown
#34
sr320
closed
4 years ago
11
Provide md5 for trimmed files
#33
sr320
closed
4 years ago
8
create CCGG (MspI cut site) tracks
#32
shellywanamaker
closed
4 years ago
4
List one thing important to showcase in manuscript
#31
shellywanamaker
closed
4 years ago
2
Confirm definition and calculation of conversion efficiency
#30
hputnam
closed
4 years ago
2
Perform genome coverage analyses as in Fig. 3 of Zhou et al. 2019 Sci reports
#29
shellywanamaker
closed
4 years ago
8
generate a conical coverage track for each coral methylome using 9 samples at 5x coverage
#28
hputnam
closed
4 years ago
14
Generate a location and structure for raw and intermediate file access
#27
hputnam
closed
4 years ago
1
Map data to proper lambda genome
#26
sr320
closed
4 years ago
2
Determine if lambda mapping results are satisfactory
#25
sr320
closed
4 years ago
1
Linking Methylation and RNASeq in Sym C1 from Pact samples
#24
hputnam
closed
4 years ago
0
generate SCORs (repeats) track
#23
hputnam
closed
4 years ago
1
Create Corr Plots with new data
#22
sr320
closed
4 years ago
12
Mapping to lambda for conversion efficiency
#21
hputnam
closed
4 years ago
3
Map reads and extract methylation for Pact reads against C1 Symbiodinium genome
#20
hputnam
closed
4 years ago
4
Update Meth_Compare_Pipeline.md with mapping code
#19
shellywanamaker
closed
4 years ago
0
update stats table with multiqc data from .bams from full alignment
#18
shellywanamaker
closed
4 years ago
3
Run multiqc on .bams from full alignments
#17
shellywanamaker
closed
4 years ago
2
CG tracks - create track and evaulate CG coverage for each method
#16
mgavery
closed
4 years ago
8
update stats table(s) with new trimming results
#15
shellywanamaker
closed
4 years ago
1
Confirm satisfaction with TrimGalore output
#14
sr320
closed
4 years ago
27
Run bioinformatics on Trim Galore Samples
#13
sr320
closed
4 years ago
4
Run Trim Galore on all samples
#12
sr320
closed
4 years ago
9
Think about methods for linking isoform and methylation information
#11
yaaminiv
closed
4 years ago
1
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