Keren Zhou

Can the input motifs be in the PWM format?

3

Hi, can the input motifs be in the PWM format? Like outputs from HOMER program (motif1.motif), an example please check bellow: ```bash >TGCATG 1-TGCATG,BestGuess:hsa-miR-4262 MIMAT0016894 Homo sapiens miR-4262 Targets (miRBase)(0.647)...

Can I apply cisTarget to estimate the RBP-regulon?

6

Hi, I have binding sites of RNA binding proteins (RBP) analyzed from CLIP-seq data, so I want to do the motif enrichment and RBP-regulon prediction, which's used as input for...

--model 'transformer_r10.4.1_5khz_v4.3' has error "UnboundLocalError: local variable 'model' referenced before assignment "

1

when running `deepmod2 detect --model 'transformer_r10.4.1_5khz_v4.3'`, it throws error like: > Traceback (most recent call last): File "/hpcf/authorized_apps/rhel8_apps/deepmod2/install/deepmod2-env2/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/hpcf/authorized_apps/rhel8_apps/deepmod2/install/deepmod2-env2/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args,...

Error found when preparing "var.tile.mtx" in the tutorial

4

`> var.tile.mtx