kundajelab chipseq_pipeline issues

kundajelab / chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

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

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issues

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Bump numpy from 1.11.3 to 1.22.0

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

#51 dependabot[bot] closed 2 years ago
1
JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa"

#50 liliaevgeniou opened 4 years ago
1
mm10

#49 jloupe closed 5 years ago
1
ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through

#48 yingsun-ucsd closed 5 years ago
25
Citing the AQUAS Pipeline

#47 mkleyman closed 6 years ago
1
Documentation for macs2?

#46 concatenize closed 6 years ago
2
Some reps get ERROR:root:--extsize must >= 1!

#45 jloupe closed 6 years ago
2
Can't download hg19 genome data

#44 tfchipchip opened 6 years ago
2
pipeline deprecated?

#43 ceesu closed 6 years ago
2
Missing `-c` for `macs2 peakcall` ?

#42 Avsecz closed 6 years ago
1
[Error] two same tag align file in (z)cat and shuf in pipe

#41 cjhong closed 6 years ago
1
job submission command

#40 LiangMa2017 opened 6 years ago
2
dead loop

#39 LiangMa2017 closed 6 years ago
18
[fread] Unexpected end of file (bwa_sai2sam_pe_core)

#38 sbstatgen closed 6 years ago
6
Fatal error: chipseq.bds, line 1354, pos 2. Task/s failed.

#37 easwaranramamurthy closed 6 years ago
4
ERROR:root:--extsize must >= 1!

#36 zzy1002081237 closed 6 years ago
2
"-q [SLURM_ACCOUNT_NAME]" interpreted as file

#35 jchap14 closed 6 years ago
1
shuf: end of file

#34 sbstatgen closed 6 years ago
8
Read length

#33 jloupe closed 6 years ago
2
Trimmed data-sets

#32 pixelRaquel opened 6 years ago
1
aquas_chipseq pipline SPP error

#31 fengyun198503 closed 6 years ago
6
aquas_chipseq pipline idr error

#30 adroubsa closed 6 years ago
4
phantompeakqualtools missing from install_dependencies

#29 jloupe closed 6 years ago
3
JSON key error in example config

#28 kdemuren closed 6 years ago
1
chipseq pipeline set up

#27 LiangMa2017 closed 6 years ago
0
Fixed error in out filename generation in bwa_aln(), bwa_sam() and bwa_sam_PE()

#26 tleonardi closed 6 years ago
0
.fq extension not removed from prefix in bwa alignement step

#25 tleonardi closed 6 years ago
0
Undefined symbol: PyUnicodeUCS2_AsASCIIString

#24 PFRoux closed 6 years ago
12
permission denied / file not found

#23 michdass closed 6 years ago
11
SPP error in one replicate

#22 dgoekbuget closed 6 years ago
2
Suggestion on how to analysis the ChIP-seq data

#21 yingsun-ucsd opened 7 years ago
0
Fatal error: /TF_chipseq_pipeline/chipseq.bds, line 1529, pos 2. Task/s failed.

#20 yingsun-ucsd closed 7 years ago
5
more than 2 replicates can not be used for chips_pipeline

#19 yingsun-ucsd closed 6 years ago
3
NA

#18 biomystery closed 7 years ago
1
Issue with bds

#17 urjaswita closed 7 years ago
4
How to modify bds if my SGE cluster using vf=memory,p=n_cpu?

#16 huboqiang closed 7 years ago
1
MACS2 KeyError

#15 da-bar closed 6 years ago
2
Fatal error: TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed.

#14 rdali closed 7 years ago
22
Installing Genomes: TwoBitToFa not found

#13 AHCChan closed 6 years ago
5
phantompeakqual Error in names(cc) < names(otl) :attempt to set an attribute on NULL

#12 crazyhottommy opened 7 years ago
0
Building custom genome data

#11 wuwill closed 6 years ago
8
Add missing pyfaidx package in requirements.txt

#10 emi80 closed 7 years ago
0
Fatal error: /data/fmao/soft/chipseq_pipeline/modules/graphviz.bds, line 126, pos 18. Trying to access element number 1 from list 'etc' (list size: 1).

#9 maofengbiao closed 6 years ago
1
software installation

#8 wcstcyx closed 7 years ago
0
Merge sambamba branch

#7 chrisprobert closed 8 years ago
0
fix command line arguments typo (?)

#6 alaindomissy closed 8 years ago
0
Update bgd to bw conversion in callpeak_macs2.bds

#5 florianduclot opened 8 years ago
2
Modified the trimming code to require an adapter, and to use cutadapt

#4 nboley closed 7 years ago
0
Explicitly set `_JAVA_OPTIONS` before calling Picard

#3 chrisprobert closed 8 years ago
0