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kundajelab
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atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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slopBed chromsizes filter on raw MACS2 output
#51
vervacity
opened
7 years ago
3
Error in ATAqC (ValueError: all the input array dimensions except for the concatenation axis must match exactly)
#50
mdurante1
closed
7 years ago
27
Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff < : missing value where TRUE/FALSE needed
#49
jfertaj
closed
7 years ago
4
Instability in mouse TSS enrichment annotations for ATAqC
#48
vervacity
closed
7 years ago
0
Overlap of DHS and ATAC-Seq peaks
#47
kostasrouskas
closed
7 years ago
4
Error with `true_rep` parameter
#46
jenchien
closed
7 years ago
6
/path/to/atac.bds.20170323_113836_801_parallel_139/task.ataqc.ataqc_rep1.line_112.id_93.sh: line 24: /path/to/atac_dnase_pipelines/ataqc/run_ataqc.py: No such file or directory
#45
jet456
closed
7 years ago
2
Invalid literal error in ATAQC step
#44
tmshaver
closed
7 years ago
0
slurm partition, result names and fatal error
#43
JensKeilwagen
closed
7 years ago
20
Add option to specify customized $TMP directory
#42
fuxialexander
closed
7 years ago
2
ataqc error in hg38: tn5.tagAlign.gz has inconsistent naming convention for record
#41
jenchien
closed
7 years ago
6
Python egg cache directory error
#40
jet456
closed
7 years ago
11
error in plotGC function
#39
victor2410
closed
7 years ago
2
no idr?
#38
jusu-E404
closed
7 years ago
6
typo in "install_genome_data.sh"
#37
jusu-E404
closed
7 years ago
1
Fix issues with adapter trimming
#36
csfoo
closed
7 years ago
0
Low TSS Enrichment Scores
#35
rleylek
closed
7 years ago
4
ERROR [ file 'atac.bds', line 1304 ] : Function parse_align_log_to_html(string,string[],string[],string[]) cannot be resolved
#34
jet456
closed
7 years ago
2
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found
#33
jenchien
closed
7 years ago
14
issue with linking packages ?
#32
jusu-E404
closed
7 years ago
7
Error: hg19 bowtie2 index
#31
rleylek
closed
7 years ago
9
preseq dependency error
#30
rfarouni
closed
7 years ago
3
problem installing genome
#29
jusu-E404
closed
7 years ago
8
Conda install prevents modules from loading
#28
kdemuren
closed
7 years ago
0
Missing config file entry 'sge.pe'
#27
boxiangliu
closed
8 years ago
2
Fix numpy openblas bug
#26
chrisprobert
closed
8 years ago
0
start adding sacCer3 genome
#25
chrisprobert
closed
8 years ago
0
Fixing dependency syntax problem with graphviz
#24
MikeDacre
closed
8 years ago
2
Error: V plot index is missing
#23
jusu-E404
closed
8 years ago
3
error at CollectGCBiasMetrics step
#22
DoaneAS
closed
6 years ago
1
Bioconda now uses build 4 of picard 1.126
#21
yunhailuo
closed
8 years ago
0
Add support for sambamba option in ataqc
#20
chrisprobert
closed
8 years ago
0
Parse alignment logs, stop pipeline if an alignment error occurs
#19
chrisprobert
closed
8 years ago
2
Remove Picard from the pipeline
#18
chrisprobert
closed
7 years ago
6
Add option for separating out technical replicates
#17
nboley
opened
8 years ago
4
Sanity check specified adapter
#16
nboley
closed
7 years ago
0
Speedup TODOS
#15
nboley
opened
8 years ago
0
Use trim_galore for paired end sequencing
#14
nboley
closed
7 years ago
0
Define a default nthreads parameter
#13
nboley
closed
8 years ago
5
Use sambamba when available for multi-threaded sorting
#12
nboley
closed
8 years ago
1
Adapter trimming gzipping should happen in parallel
#11
nboley
closed
8 years ago
1
use pigz instead of gzip when available
#10
nboley
closed
8 years ago
1
re-write trim adapters
#9
nboley
closed
8 years ago
2
Install script doesn't stop when it encounters errors
#8
nboley
closed
8 years ago
1
update env file for scg4
#7
chrisprobert
closed
8 years ago
0
The default value of idr_thresh is wrong
#6
chrisprobert
closed
8 years ago
3
clarify in helpstring that -align option skips ataqc
#5
chrisprobert
closed
8 years ago
1
Do we need additional arguments for ATACseq?
#4
nboley
closed
8 years ago
1
add replicate index for bam file path
#3
chrisprobert
closed
8 years ago
0
"-species" flag seems to be required
#2
nboley
closed
8 years ago
1
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