parkerlab / atactk Goto Github PK

Hi,
I was reading, and got to know that one has to shift +4bp and -5bp for the reads on + and - strand for TF footprint https://sites.google.com/site/atacseqpublic/atac-seq-analysis-methods/offsetmethods

does atactk make_cut_matrix expects the un-shifted bam or shifted bam? http://atactk.readthedocs.io/en/latest/usage.html#creating-atac-seq-signal-plots-for-motifs.
GreenleafLab/NucleoATAC#58

Thanks!
Tommy

I didn't get the point. It feels that this method tends to produce higher counts around the motif boundary, and then lower counts inside the motif, which makes it like a valley.

Thanks,
Yichao

Hi, thanks for providing such a good tool.

Would it be possible to add an option to count the cut sites instead of the midpoints of each fragments in measre_signal script?

Thanks.

Jason

Hi,

When I run the make_cut_matrix program, I get an error that reads:

2016-08-01 13:47:14,478 ERROR 'extra_fields'
Traceback (most recent call last):
File "/net/bmc-pub7/data2/boyerlab/users/kdemuren/lib/python2.7/site-packages/atactk-0.1.5-py2.7.egg/EGG-INFO/scripts/make_cut_matrix", line 235, in make_cut_matrix
for motif_count, (motif, row, tree) in enumerate(results, 1):
File "/net/bmc-pub7/data2/boyerlab/users/kdemuren/lib/python2.7/site-packages/atactk-0.1.5-py2.7.egg/EGG-INFO/scripts/make_cut_matrix", line 232, in
results = (score(motif) for motif in motifs)
File "/home/kdemuren/lib/python2.7/site-packages/atactk-0.1.5-py2.7.egg/atactk/data.py", line 212, in read_features
del row['extra_fields']
KeyError: 'extra_fields'

My command syntax was:

make_cut_matrix -d -b '(36-149 150-324 325-400 1)' CM_ATAC_rep1_1_1.bam MA0052_matches.bed.gz | gzip -c > MEF2A.discrete.matrix.gz

Any suggestions on how to fix this?

Thanks for your time,
Kunle

Hi, rdalbanus，thanks for providing such a good tool.

(cutruntools2.1) chenzhiyi@luo-lab-tower:~/Software/CUT-RUNTools-2.0-master/install$ /home/chenzhiyi/.local/bin/make_cut_matrix -v -b '(25-150 1)' -d -o 0 -r 100 -p 1 -f 3 -F 4 -F 8 -q 0 /media/dell/data2/chenzhiyi/bulk-example-test/PRDM9/aligned/dedup.120bp/PRDM9.bam fimo.bed > fimo.cuts.freq.txt
Traceback (most recent call last):
File "/home/chenzhiyi/.local/bin/make_cut_matrix", line 277, in
make_cut_matrix(parse_arguments())
File "/home/chenzhiyi/.local/bin/make_cut_matrix", line 182, in parse_arguments
return parser.parse_args()
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1734, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1766, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1972, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1912, in consume_optional
take_action(action, args, option_string)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1824, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 2265, in _get_values
value = self._get_value(action, arg_string)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 2294, in _get_value
result = type_func(arg_string)
File "/home/chenzhiyi/.local/lib/python3.6/site-packages/atactk/command.py", line 126, in parse_bins
bin_string = bin_string.value()
AttributeError: 'Symbol' object has no attribute 'value'