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Hi Jacob,
I'm using ChromBPnet to examine some ATAC-seq data, and I have a general question about preprocessing.
In the data processing section from the original ATAC-seq paper (Buenrostro et al…
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Hello,
It looks like SELMA has built-in bias score matrices for DNaseI and Tn5, each called by the '-t DATATYPE' flag. Is it possible for the user to generate/use custom bias matrices for other enz…
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### Project short name:
GSE132065_BloodTimeHuman
### Primary Wrangler: @ipediez
Enrique
### Secondary Wrangler:
### Associated files
* Google Drive: https://drive.google.com/drive/folders/1LuId…
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## **Describe the bug**
Hi team,
I tried to peak-call using input files as dedupped BAM files. It worked initially for 1 sample (2 replicates), but not for the second sample.
## **OS/Platform**…
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Hello. Your code **dataset.py** shows the process of building your data. However, you don't seem to have given a simple example to show temp_seq, temp_dnase and temp_labels. e.g. what kind of informat…
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hello!great job! 理论上来说在下游任务的微调阶段,只用到了预训练backbone的encoder部分,只需要序列输入得到representation,那么为什么在EPCOT_usage里面还需要dnase文件作为输入呢。。。
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I am trying to incorporate `librarian` into our [quality-check-standard pipeline](https://github.com/stjudecloud/workflows), but there doesn't seem to be a feasible way to run this at scale.
* I assu…
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Hello, I'm trying to replicate your prediction results for "CD4-positive_helper_T_cell-ENCODE" published in [Nature at 2021](https://www.nature.com/articles/s41586-021-03446-x#Sec9): as shown in the […
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Hello,
Executed code:
shapemapper --name example --target ../FASTA/RNA.fasta --out RNA_shapemap --amplicon --modified --R1 100mM_1M7_RNA_R1.fastq --R2 100mM_1M7_RNA_R2.fastq --untreated --R1 DM…