broadinstitute gtex-pipeline issues

broadinstitute / gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

BSD 3-Clause "New" or "Revised" License

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issues

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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