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broadinstitute
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gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
BSD 3-Clause "New" or "Revised" License
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run_rnaseqc.py unrecognized arguments: --unpaired
#102
yingsun-ucsd
opened
2 weeks ago
0
error message showing "check that the path exists and you have write permission for this file." But it does not make sense.
#101
yingsun-ucsd
closed
2 months ago
1
Building the indexes Issue (drive mapping issue maybe 【docker run "-v" ...】)
#100
yingsun-ucsd
closed
2 months ago
5
AttributeError: module 'qtl.io' has no attribute 'sort_bed'
#99
isaartiga
opened
3 months ago
0
Update run_STAR.py
#98
abhiachoudhary
closed
6 months ago
0
GTEx release V10
#97
AEstebanMar
opened
6 months ago
0
Create pre_RSEM_processing.wdl
#96
abhiachoudhary
closed
6 months ago
0
Update star_index.wdl
#95
abhiachoudhary
closed
6 months ago
0
Update star.wdl
#94
abhiachoudhary
closed
6 months ago
0
Update run_STAR.py
#93
abhiachoudhary
closed
6 months ago
0
Update star.wdl
#92
abhiachoudhary
closed
6 months ago
0
Update run_STAR.py
#91
abhiachoudhary
closed
6 months ago
0
Added rsem preprocessing file
#90
abhiachoudhary
closed
6 months ago
0
Added new dockerfile and run_remove_IDS_reads.sh to v10pg
#89
abhiachoudhary
closed
6 months ago
0
Added aligning step
#88
abhiachoudhary
closed
7 months ago
0
error with eqtl_expression.py
#87
jfertaj
closed
1 week ago
1
Package versions between README.md and Dockerfile differ
#86
VangelisTheodorakis
opened
1 year ago
0
Syntax error
#85
qicaibiology
closed
1 week ago
1
How to install Bamsync
#84
zhangpicb
closed
1 year ago
0
skip empty annotations
#83
jvolkening
opened
1 year ago
0
sample_participant_lookup file -> Genotype and Phenotype are not matching
#82
SynaSpike
closed
1 year ago
2
Missing files and script errors
#81
geng-lee
closed
1 year ago
1
A default for GTEx run_PEER.R doesn't match the PEER library default
#80
kshakir
opened
1 year ago
0
access to gtex-resources on google cloud
#79
limrock1
closed
1 week ago
1
Population-based phasing reference panel
#78
teng-gao
closed
1 year ago
1
geTMM normalization
#77
ActioTom
opened
2 years ago
0
missing "qtl" module in leafcutter prepare script
#76
lw157
closed
2 years ago
0
The script does not seem to work with Ensembls GRch38 release-105 GTF file
#75
bishwaG
closed
2 years ago
1
add qtl package to leafcutter Dockerfile
#74
yfarjoun
closed
2 years ago
0
RNA-SeQC v10 returning all zero counts
#73
raplayer
closed
2 years ago
1
criterion or cut-off used in GTEx v8.signif_variant_gene_pairs.txt
#72
Shicheng-Guo
closed
2 years ago
1
provide workbench links
#71
leipzig
opened
3 years ago
0
Bug fix to gzip call so the correct filepaths are passed in.
#70
manwayl
closed
3 years ago
0
torus fastqtl input file
#69
cindywen96
closed
3 years ago
2
Updates for V10 pipeline
#68
francois-a
closed
3 years ago
0
rnaseq_pipeline_fastq/bam reference invalid import
#67
jdidion
closed
3 years ago
5
Update README.md
#66
leipzig
closed
3 years ago
0
ISO test inputs.json
#65
leipzig
opened
3 years ago
0
PEER factors as oppose to surrogate variables
#64
montenegrina
opened
3 years ago
0
Update rnaseq_pipeline_fastq.wdl
#63
leipzig
closed
3 years ago
0
Bugfixes
#62
dampierch
opened
3 years ago
1
Add pyqtl to qtl/Dockerfile so eqtl_prepare_expression.py runs smoothly
#61
dampierch
closed
2 years ago
1
collapse_annotation.py fails if the input file doesn't contain comment lines
#60
erynes
closed
3 years ago
2
run_FastQTL_threaded.py in Docker return error
#59
xiyasong
closed
3 years ago
4
Docker run eqtl_prepare_expression.py with no error but didn't generate expression.bed.gz file
#58
xiyasong
closed
3 years ago
2
What's the difference between gencode.vXX.GRCh38.genes.gtf and gencode.vXX.GRCh38.genes.collapsed_only.gtf?
#57
xiyasong
closed
3 years ago
4
Which RNA-SeQC version should be used now and what's RSEM results used for?
#56
xiyasong
closed
3 years ago
2
Could not open genomeFastaFile:/data/Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta
#55
xiyasong
closed
3 years ago
2
Question about the eQTL pipeline
#54
nelsonchanhk
closed
3 years ago
1
Output files from rnaseq v8 pipeline
#53
nelsonchanhk
closed
3 years ago
4
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