Run BPnet with one input bw track #18
Comments
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Yan,
Ziga might be able to give you some insights on how to adapt the current
repo to support unstranded inputs. But I wanted to give you some additional
information.
The ChIP-exo/nexus/seq BPNet architecture is not optimized for
ATAC-seq/DNase-seq data. The model needs to be expanded and tweaked a bit
to get the best out of it for ATAC-seq/DNase-seq. Also bias correction
using enzyme bias tracks is quite important.
Also this particular repo is not being extended to support these additional
data types. While the current repo is and will continue to be the primary
repo associated with the BPNet paper, we are transitioning to this repo
https://github.com/kundajelab/basepairmodels for longer term support and
extensions to ATAC-seq, DNase-seq, histone ChIP-seq and many additional
post-processing frameworks which are coming soon (within 2 months).
Thanks,
Anshul.
…On Mon, Feb 1, 2021 at 2:16 PM yanwang271 ***@***.***> wrote:
Hi,
I am trying to use bpnet on ATAC-seq data and there is one track for each
tasks.
When I run bpnet chip-nexus-analysis, I got errors:
0%| | 0/11 [00:00<?, ?it/s]/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py:130: UserWarning: region counts not present. Returning the default contribution scores
warnings.warn("region counts not present. Returning the default contribution scores")
100%|██████████| 11/11 [00:35<00:00, 3.20s/it]
0%| | 0/11 [00:00<?, ?it/s]Traceback (most recent call last):
File "/bpnet/bin/bpnet", line 8, in <module>
sys.exit(main())
File "/bpnet/lib/python3.6/site-packages/bpnet/__main__.py", line 38, in main
argh.dispatch(parser)
File "/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/bpnet/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
result = function(*positional, **keywords)
File "/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 905, in chip_nexus_analysis
footprint_width=footprint_width)
File "/bpnet/lib/python3.6/site-packages/bpnet/cli/modisco.py", line 722, in modisco_table
df = modisco_table(data)
File "/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py", line 199, in modisco_table
for pattern in tqdm(data.mf.pattern_names())])
File "/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py", line 199, in <listcomp>
for pattern in tqdm(data.mf.pattern_names())])
File "/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py", line 220, in pattern_features
for res in pattern_task_features(pattern, task, data)] +
File "/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py", line 220, in <listcomp>
for res in pattern_task_features(pattern, task, data)] +
File "/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py", line 278, in pattern_task_features
("footprint", task_footprint(pattern, task, data)),
File "/bpnet/lib/python3.6/site-packages/bpnet/modisco/table.py", line 322, in task_footprint
("strandcor", correlate(agg_profile_norm[:, 0], agg_profile_norm[::-1, 1]).max()),
IndexError: index 1 is out of bounds for axis 1 with size 1
I thought this is because that there is only one track in
agg_profile_norm. To run the programme, I changed the line 322 in
bpnet/modisco/table.py to ("strandcor", correlate(agg_profile_norm[:],
agg_profile_norm[::-1]).max()). I know doing this will change the
"strandcor" value. So, I am wondering whether it is okay to do changes like
this, and how much this will affect the motif discovery and the further CWM
scan step? Or, is there another way to run the programme with only one bw
track?
Thanks in advance for your help!
Best,
Yan
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Hi Yan, +1 to what Anshul wrote. It's the plotting code that breaks with single-stranded tracks when trying to run Note that |
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Hi @akundaje , Thanks for your replay. I really look forward to trying the new version! |
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Hi @Avsecz , Thanks for the remarks! Now I know I can use the cwm-scan directly after modisco-run. |
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Hi,
I am trying to use bpnet on ATAC-seq data and there is one track for each tasks.
When I run
bpnet chip-nexus-analysis, I got errors:I thought this is because that there is only one track in agg_profile_norm. To run the programme, I changed the line 322 in bpnet/modisco/table.py to ("strandcor", correlate(agg_profile_norm[:], agg_profile_norm[::-1]).max()). I know doing this will change the "strandcor" value. So, I am wondering whether it is okay to do changes like this, and how much this will affect the motif discovery and the further CWM scan step? Or, is there another way to run the programme with only one bw track?
Thanks in advance for your help!
Best,
Yan
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