qukunlab / atac-pipe Goto Github PK

I want to add other motif for foorprint step, could you tell where could I download ?

I don't know what file the '--group' need. Can someone give me a example pls? Thanks.

I was comparing 2 samples but stuck in step 1. Everything seems fine until Quality control.
What do you think the problem is? Thanks.
`Runtime.totalMemory()=1073217536
Convert chrM.sam to chrM.bam for D87
Convert chrM.sam to chrM.bam for T87
Draw TSS enrichment plot for D87
Draw TSS enrichment plot for T87
Draw fragment distribution plot for D87
Draw fragment distribution plot for T87
Quality control D87
Quality control T87

Traceback (most recent call last):
File "atac-pipe.py", line 703, in
main()
File "atac-pipe.py", line 690, in main
if options.MappingQC: MappingQC()
File "atac-pipe.py", line 283, in MappingQC
pool.map(MappingQC_6, sn)
File "/zhaowei/YJM/miniconda3/envs/atac-pipe/lib/python2.7/multiprocessing/pool.py", line 253, in map
return self.map_async(func, iterable, chunksize).get()
File "/zhaowei/YJM/miniconda3/envs/atac-pipe/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
AttributeError: 'NoneType' object has no attribute 'group'`

We modified some parameter commands in the old version so that we can better use ATAC-pipe. Previous versions may not be able to correctly pair double-ended files of the same sample in some cases. Now this problem has been solved very well.

I want to use other reference genomes(maize genome),but this pipeline only offers ‘hg19’ and ‘mm9’ as genome references. I wonder if there is a way to add others reference genomes to this pipeline.

got this issue when running command python atac-pipe.py:

Traceback (most recent call last):
  File "atac-pipe.py", line 8, in <module>
    import levenshtein
ImportError: No module named levenshtein

what do you think went wrong?