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neurogenomics
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CUT_n_TAG
Preprocessing pipeline for CUT&TAG data.
MIT License
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Test effects of removing mito reads on peak calling with additional samples
#46
leylaabbasova
closed
1 year ago
0
Calculate duplicate FRiPs
#45
leylaabbasova
opened
1 year ago
1
Add mito % for all samples to Supplementary table 2
#44
leylaabbasova
closed
1 year ago
0
Make sample tracks available online
#43
leylaabbasova
opened
1 year ago
2
Add ENCODE IDs in text
#42
leylaabbasova
opened
2 years ago
0
Edit text to accommodate figure changes
#41
leylaabbasova
closed
1 year ago
0
Make ENCODE bigwigs
#40
leylaabbasova
closed
1 year ago
0
Improve legibility
#39
leylaabbasova
closed
1 year ago
0
Re-run and re-plot read correlations with me3 broad peaks and ENCFF000BXA
#38
leylaabbasova
closed
1 year ago
0
Add TSA samples to Supp Table 1
#37
leylaabbasova
closed
1 year ago
0
Add total peaks called to TSA panel
#36
leylaabbasova
closed
1 year ago
0
Re-plot tidier TSA figures
#35
leylaabbasova
closed
1 year ago
0
Test how removing mitochondrial reads from top sample affects peak calling
#34
leylaabbasova
closed
1 year ago
0
Re-plot PCR cycle test results downsampled
#33
leylaabbasova
closed
1 year ago
0
Plot PCR cycle test results at full read depth
#32
leylaabbasova
closed
1 year ago
0
Update Supp Table 1 to include PCR test and TSA samples
#31
leylaabbasova
closed
1 year ago
0
Clarify that: 1) FRiPs analysis shows comparisons of CUT&Tag reads in CUT&Tag peaks (and 42% refers to ENCODE reads in ENCODE peaks); 2) Supplementary figures are expanded to include all samples
#30
leylaabbasova
closed
1 year ago
0
Reshuffle to add TSA and PCR cycle results to Fig 2 (preceding QC figure)
#29
leylaabbasova
opened
2 years ago
0
Plot IgG results for reviewer - only did ENCODE capture for SEACR and MACS2
#28
leylaabbasova
closed
1 year ago
0
Plot differences in peak widths between callers - all and promoter-overlapping
#27
leylaabbasova
closed
1 year ago
0
Add IGV peak closeups to supplementary
#26
leylaabbasova
closed
1 year ago
0
Add full TF analysis figure with both SEACR and MACS2 results to supplementary + comment on similarities/differences?
#25
leylaabbasova
closed
1 year ago
0
Calculate + plot FRiPS in intersecting ENCODE/C&T peak regions (for both ac and me3, merged and separate reps)
#24
leylaabbasova
closed
1 year ago
0
Reprocess and analyse HCT116 me3 data (https://rupress.org/jcb/article/220/12/e202103078/212821/High-throughput-single-cell-epigenomic-profiling)
#23
leylaabbasova
closed
1 year ago
0
Check % of mitochondrial reads
#22
leylaabbasova
closed
1 year ago
0
Call consensus peaks on all our C&T samples
#21
bschilder
closed
1 year ago
2
Compare our CUT&TAG datasets against on/off-target ENCODE histone modification data: are H3K27ac datasets from all antibodies / analysis pipelines, always more similar to ENCODE H3K27ac, than to other ENCODE histone mods?
#20
bschilder
closed
2 years ago
0
Examine data from scCUT&TAG... which fraction of reads that would otherwise be considered duplicates, are assigned to different cells? This would help us evaluate whether duplicates should be kept + how much they need to be minimised.
#19
bschilder
closed
2 years ago
0
Establish use of a CUT&TAG analysis pipeline that can be run easily on the Imperial cluster
#18
bschilder
closed
2 years ago
0
Begin drafting paper outline
#17
bschilder
closed
2 years ago
0
Update README with links Leyla's latest rmarkdown html outputs
#16
bschilder
closed
3 years ago
0
Set up single-cell analysis pipeline
#15
bschilder
closed
2 years ago
1
Test the effects of read depth
#14
bschilder
closed
3 years ago
0
Generate Precision-Recall curves
#13
bschilder
closed
3 years ago
0
Rerun SEACR using different thresholds
#12
bschilder
closed
3 years ago
0
Share MPRA data
#11
bschilder
closed
3 years ago
1
Conduct genome-wide correlation analyses with binning
#10
bschilder
closed
3 years ago
0
Re-analyze Henikoff and ENCODE samples using our pipeline
#9
bschilder
closed
3 years ago
0
Run nf-core/cutandrun pipeline
#8
bschilder
closed
2 years ago
1
Can't run nf-core/atacseq test example
#7
bschilder
closed
2 years ago
4
Process `get_software_versions` terminated with an error exit status (255)
#6
bschilder
closed
2 years ago
6
nf-core/atacseq on HPC: "Job resource selection does not match any permitted configuration"
#5
bschilder
closed
3 years ago
4
run nf-core/ataceq on CUT&TAG
#4
bschilder
closed
2 years ago
1
Compare CUT&TAG vs. ENCODE
#3
bschilder
closed
3 years ago
1
Try using Henipipe on Imperial cluster and keep script for loading modules etc required to get it to run
#2
NathanSkene
closed
2 years ago
0
Try using NF-Tower with the NF-ATAC pipeline
#1
NathanSkene
closed
3 years ago
0