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Hi Dave (@davek44 ),
I recently read your 2018 Basenji paper, where you referred to cell-type-specific gene expression. In the paper, you mentioned that you made predictions in the 128-bp bin conta…
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Hi,
I'm trying to run F-Seq2 on 3' RNA single end sequencing data to identify polyadenylation peaks. I'm running the following
```
fseq2 callpeak input.bam -chrom_size_file mm10.chromsizes.bed …
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MACS2 is wonderful, thank-you for it. I hope it becomes a paper to be referenced at some point.
I've only just noticed that while the README says the default q-vlaue is 0.01, that in the MACS2 (2.…
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Hi,
I have gone through the other two ATAC-seq issues. Accordingly, I tried one run with BAMPE and one without. here are the codes.
``macs2 callpeak -t raw/dH1f_1.bam -n dh1f_1.broad -g hs -q 0.05…
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Deep learning methods are notably difficult to interpret. If data is provided without explicitly engineered features, how are you going to address finding any biases in predictions?
What sort of p…
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Hello,
If I want to run Leopard with my own data, what should I place in `Leopard/data/`. Also, I couldn't find anything about `avg.bigwig` file, which is hardcoded in `predict.py`
Thanks
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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:
```
0%| | 0/11 [00:00
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Hi,
I am trying to use msCentipede on a ATAC-seq time course series without success. I get an error when running a command like
python call_binding.py --task learn --protocol ATAC_seq testbk/Ctcf_…
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The current negative sets are leading the model to overfit on training data and to generalize poorly to validation data. The current negative sets are generated by identifying peaks that are absent in…
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Are there any guidelines on the memory consumption of createASVCF.sh? I've run out of memory even when allocating 150GB. I don't really know how to best tell if this is normal or if I'm doing somethin…