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NCI-RBL
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iCLIP
RNA Biology Pipeline to Characterize protein-RNA Interactions
https://rbl-nci.github.io/iCLIP/
MIT License
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QC dir error in rule QC BARCODES
#152
slsevilla
closed
1 year ago
1
complete feature branch merge
#151
slsevilla
closed
1 year ago
0
Add alternative peak caller (CTK)
#150
wilfriedguiblet
opened
1 year ago
1
Transcriptome mapping
#149
wilfriedguiblet
closed
1 year ago
0
Add Mapping to Transcriptome
#148
wilfriedguiblet
closed
1 year ago
2
limitOutSJcollapsed default value is too low for some samples
#147
slsevilla
closed
1 year ago
1
Active dev
#146
slsevilla
closed
1 year ago
0
Expected barcode count does not include samples with lower than average number of reads
#145
slsevilla
closed
1 year ago
1
Troubleshooting project: 1-5-22_PUF60iCLIP
#144
slsevilla
closed
1 year ago
3
sync main and activDev
#143
slsevilla
closed
1 year ago
0
STAR memory failure - likely due to mismatch of SAMTOOLS sort and cluster memory requirements
#142
slsevilla
closed
1 year ago
1
Create CPM/FPKM fold change calculation output for files
#141
slsevilla
opened
1 year ago
1
When expected barcodes do not match observed barcodes error file does not stop pipeline
#140
slsevilla
closed
1 year ago
1
Expected barcode count does not change with large sample sizes
#139
slsevilla
closed
1 year ago
2
create v2.2.1
#138
slsevilla
closed
1 year ago
0
issue with config parsing spaces
#137
slsevilla
closed
1 year ago
1
Control version of snakemake
#136
slsevilla
closed
1 year ago
1
Merge new workflow image
#135
slsevilla
closed
1 year ago
0
merge code changes for v2.2
#134
slsevilla
closed
1 year ago
0
Create Lucidchart of pipeline
#133
slsevilla
closed
1 year ago
3
Pipeline continues to run even if most reads do not map
#132
slsevilla
closed
1 year ago
1
merging wilfried's changes into activeDev
#131
slsevilla
closed
2 years ago
0
Active dev merge for v2.0 (updated)
#130
slsevilla
closed
2 years ago
1
-M and -W flags added to MANORM
#129
slsevilla
closed
1 year ago
0
Update 05_peak_annotation_functions.R
#128
wilfriedguiblet
closed
2 years ago
0
DE issues with Marco's run 8-09-21-HaCaT_fCLIP_v2.0
#127
slsevilla
closed
1 year ago
10
Error creating DAG of pipeline
#126
slsevilla
closed
2 years ago
1
improve annotation in pipeline
#125
slsevilla
opened
2 years ago
3
dedup failing without error message
#124
slsevilla
closed
2 years ago
1
merge changes for v2.0
#123
slsevilla
closed
2 years ago
0
add Mapping statistics to QC Report
#122
slsevilla
closed
2 years ago
1
add FASTQ SCREEN results to multiqc report
#121
slsevilla
closed
2 years ago
1
MANORM_beds searching for beds that have already been gzipped
#120
slsevilla
closed
2 years ago
3
determine the impact of seedPerwindowNmax on samples
#119
slsevilla
closed
2 years ago
1
Snakemake re-runs rules when any part of rule is changed
#118
slsevilla
closed
2 years ago
2
annotation bed has incorrect number of fields
#117
slsevilla
closed
2 years ago
3
seedPerwindowNmax bug in STAR
#116
slsevilla
closed
2 years ago
7
Segmentation fault when running STAR
#115
slsevilla
closed
2 years ago
5
MANORM can't move folder to location where files exist
#114
slsevilla
closed
2 years ago
1
BAM BIN discrepancy during STAR alignment
#113
slsevilla
closed
2 years ago
3
EOF error during sort_index_stats
#112
slsevilla
closed
2 years ago
4
test PURECLIP peak calling
#111
slsevilla
closed
2 years ago
1
Investigate overhangs and GAPS
#110
slsevilla
closed
2 years ago
1
fix tmp error
#109
slsevilla
closed
2 years ago
1
Active dev
#108
slsevilla
closed
2 years ago
0
Replace iCOUNT with Ultraplex
#107
kopardev
closed
2 years ago
2
Replace Novoalign by STAR
#106
kopardev
closed
2 years ago
2
Investigate different STAR parameters
#105
kopardev
closed
2 years ago
6
dedup requirements
#104
slsevilla
closed
2 years ago
1
remove manifest checking rule out of Snakefile
#103
kopardev
closed
2 years ago
2
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