aryarm as_analysis issues

aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

MIT License

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issues

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Specify in docs that vcf file needs accompanying index file

#79 zrcjessica opened 3 years ago
1
document meaning of columns in output of R scripts

#78 aryarm opened 3 years ago
0
add config option for supporting reads cutoff

#77 aryarm opened 3 years ago
0
start on work for asoc analysis

#76 aryarm closed 3 years ago
0
priorities

#75 aryarm opened 3 years ago
0
big picture: turning this into a command line tool

#74 aryarm opened 3 years ago
1
create a small, test dataset and a testing suite

#73 aryarm opened 3 years ago
2
simplify how samples are specified

#72 aryarm opened 3 years ago
4
allow BAM files as input to the WASP subworkflow

#71 aryarm opened 3 years ago
1
Change name of column for proportion of ref allele in rna.csv.gz

#70 zrcjessica opened 3 years ago
0
add support for peak regions for ASOC analysis

#69 zrcjessica opened 3 years ago
2
add error messages for dataframes with 0 rows after filtering

#68 zrcjessica opened 3 years ago
1
remove quoting in CSVs output by R scripts

#67 aryarm opened 3 years ago
0
support for unpaired reads in the WASP subworkflow

#66 aryarm opened 3 years ago
0
support for single-end RNA-seq and ATAC-seq in the WASP subworkflow

#65 aryarm opened 3 years ago
0
allow gzipped FASTAs and GTFs when using STAR

#64 aryarm opened 3 years ago
1
extract heterozygotes from the vcf before converting to h5 files

#63 aryarm opened 3 years ago
1
preliminary support for allele specific open chromatin (ASOC) analyses

#62 aryarm closed 3 years ago
0
ATAC-seq support

#61 aryarm opened 3 years ago
1
assume GQ = 20 in the absence of GQ tags within the provided VCF

#60 aryarm closed 3 years ago
0
filter to only GQ tag before extracting GQ tags per sample

#59 aryarm opened 3 years ago
0
set disk_mb values appropriately

#58 aryarm opened 3 years ago
0
allow for linking samples from a terra bucket

#57 aryarm opened 3 years ago
2
improve dependency installation on cloud

#56 aryarm opened 3 years ago
0
preemptible instances

#55 aryarm opened 3 years ago
0
allow input as h5 files

#54 aryarm closed 4 years ago
1
skipping the variant calling pipeline within the master pipeline

#53 aryarm closed 3 years ago
1
check samples exist

#52 aryarm closed 3 years ago
1
use checkpoints instead of dynamic

#51 aryarm closed 3 years ago
1
snps that don't overlap a gene

#50 aryarm opened 5 years ago
1
LD_LIBRARY_PATH problems

#49 aryarm opened 5 years ago
2
consider extracting common rules to separate snakefile

#48 aryarm closed 3 years ago
0
r packages

#47 aryarm opened 5 years ago
0
extracting heterozygotes in rules.extract_hets

#46 aryarm closed 5 years ago
0
a report

#45 aryarm closed 4 years ago
0
download WASP for the user

#44 aryarm closed 5 years ago
1
re-attempt failed jobs and scale resource usage

#43 aryarm closed 5 years ago
2
improve use of STAR in Snakefile-WASP

#42 aryarm closed 6 years ago
0
update default env to reflect new WASP version

#41 aryarm closed 6 years ago
1
rna version of allele.imbalance script

#40 aryarm closed 6 years ago
1
consider printing progress statements in prepare_counts and find_imbalance?

#39 aryarm closed 6 years ago
0
prepare_counts uses too much memory

#38 aryarm closed 6 years ago
5
revise params

#37 aryarm closed 3 years ago
0
use of samples file prevents reruns

#36 aryarm closed 6 years ago
0
memory

#35 aryarm closed 6 years ago
2
modify our use of WASP snakemake pipeline to save space

#34 aryarm closed 6 years ago
1
SNPs only

#33 aryarm closed 6 years ago
2
incorporate R package dependencies into default conda env

#32 aryarm closed 5 years ago
0
parallelize R script

#31 aryarm closed 6 years ago
0
extract hets from WASP counts, as well

#30 aryarm closed 6 years ago
0