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Thanks for following up. In agreement with your above post, I found the pretrained model to be incompatible with my dataset and some sample ENCODE datasets. The custom trained model...

Indeed, the output is pretty impressive, especially if I set the track bounds to hide the 1.0 background:  Here is a link to the training [config](https://www.dropbox.com/sh/bm49m534jqiusrf/AADzNLbQHf-PbuDauYyhWjZaa)

Hi @avantikalal, I tried the parameters above, but the results did not look good.  I am a little concerned about the fact that, for each noisy BW, I have...

Hi @pmelsted, I'm having a similar issue with a custom GTF. Maybe these aren't compatible with kallisto? Or the wrong GFF version is used? Thanks for the help. Input: `...

Are there any instructions for the clone repo installation option? Pip installs often fail. It would be nice to be able to troubleshoot.

Thanks for the quick reply. Tabs look okay to me: >2294^IDATA/2294.dup.fix.bam^IDATA/2294.bed 2296^IDATA/2296.dup.fix.bam^IDATA/2296.bed I'm not very familiar with snakemake, so trying to execute snakefile line-by-line to debug provided limited insight: 1....

Regarding the formatting issues, I will try to re-run using your suggestions after troubleshooting the issues below. For now, the below samples worked well: >Two data/two.bam data/two.bed Three data/three.bam data/three.bed...

Hi @aryarm, Just getting back to this. The pipeline runs past the previously mentioned errors by adding read groups. Thanks for the tips! Unfortunately, I'm confronted with a more cryptic...