kundajelab atac_dnase_pipelines issues

kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

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

159 stars 81 forks source link

issues

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Bump numpy from 1.11.3 to 1.22.0

#151 dependabot[bot] opened 2 years ago
0
Bump numpy from 1.11.3 to 1.21.0

#150 dependabot[bot] closed 2 years ago
1
Error Message: "No such file or directory found: 'java': 'java'"

#149 astephen333 closed 2 years ago
2
Broken link in the README

#148 k3yavi closed 4 years ago
1
source activate fail

#147 yinshiyi opened 4 years ago
3
Location of cromwell-34.jar

#146 imk1 closed 5 years ago
1
genome hg38 install

#145 danxunLi opened 5 years ago
3
Inconsistant behavior of pipeline-runs, with same input parameters

#144 ravipatel4 opened 5 years ago
3
mm10 vs Grcm38(Gencode)

#143 pdellorusso opened 5 years ago
1
trouble installing genome data for mm10

#142 eunsolp closed 5 years ago
4
hot fix for MACS2 negative coord

#141 leepc12 closed 5 years ago
0
How to cite this ppeline

#140 sjn7 opened 5 years ago
1
differences between "new" and "old" pipeline

#139 computbiolgeek opened 5 years ago
4
Installing dependencies (bash install_dependencies.sh

#138 grrompala opened 5 years ago
1
error running on DNANexus platform

#137 llz-hiv closed 5 years ago
2
Error during ataqc step "IOError: File [xxx]R1.trim.merged.signal does not exist"

#136 Chokaro closed 5 years ago
2
Error in postalign_xcor.bds', line 102

#135 beckedorff opened 5 years ago
5
Fatal error: atac.bds, line 1200, pos 2. Task/s failed....during peakcalling

#134 grrompala opened 5 years ago
1
Input bams of multiple true replicates

#133 anthonyjpayne closed 5 years ago
0
Can I install this ATAC-pipeline in Mac?

#132 llz-hiv opened 5 years ago
16
which files created by this pipeline can be used for homer to find motifs?

#131 llz-hiv closed 6 years ago
1
SCG SLURM hg38 permissions error?

#130 mkdegorter closed 5 years ago
9
Steps between pipeline and diffE

#129 raboul101 opened 6 years ago
1
Error : Creating checkpoint file

#128 rehamFatima closed 5 years ago
25
Compile error for atac.bds

#127 DuYushen opened 6 years ago
1
Data set

#126 rehamFatima opened 6 years ago
24
Comparing Treatments with Multiple Paired End Replicates

#125 raboul101 opened 6 years ago
11
Java memory issue

#124 ahorn720 opened 6 years ago
1
Can this pipeline be used for analyzing paired-end 75bp reads?

#123 liangzhuli opened 6 years ago
1
error in loading caTools

#122 timydaley closed 6 years ago
4
shuf: read error: Cannot allocate memory at spr_tag_PE step

#121 chesi closed 6 years ago
4
queue option on Sherlock

#120 timydaley closed 6 years ago
9
stops at idr2

#119 ahorn720 closed 6 years ago
3
messy row labels on "Comparison to Roadmap DNase" plot

#118 icanwinwyz closed 6 years ago
3
Is there any difference between Conservative Set and Optimal Set of peaks?

#117 amirshams84 closed 6 years ago
2
Removing Mitochondrial hits is not consistent between replicate and pseudo replicates

#116 amirshams84 opened 6 years ago
1
Fatal error: /atac_dnase_pipelines/modules/conf.bds, line 39. Java heap space

#115 nteran opened 6 years ago
4
broadpeak calling is off

#114 fanying2015 closed 6 years ago
3
FRiP calculation absent

#113 am33567 opened 6 years ago
1
annotate peaks produced by this pipeline

#112 llz-hiv closed 6 years ago
2
Error in postalign_xcor.bds line 98

#111 am33567 closed 6 years ago
6
sbatch: error: unable to open file [account]

#110 odegoede closed 6 years ago
3
Fatal Error in call peaks when starting with tag aligns

#109 easwaranramamurthy opened 6 years ago
1
java.lang.IndexOutOfBoundsException

#108 am33567 opened 6 years ago
1
Installing genomes from local source.

#107 am33567 closed 6 years ago
4
Bowtie2 mem error？ qsub , SGE

#106 Ruismart closed 6 years ago
2
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 30

#105 sckinta opened 6 years ago
5
Trouble Installing

#104 ahorn720 closed 6 years ago
1
Error with adapter auto detection

#103 easwaranramamurthy closed 6 years ago
4
Can't kill a non-numeric process ID at /home/mycount/.bds/clusterGeneric/run.pl line 30

#102 llz-hiv closed 6 years ago
12