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# Tasks
Welcome to the HCA DCP! We are pleased to introduce you to the data wrangling team. Before beginning to work by yourself, you'll be asked to complete a set of tasks and meetings. These will …
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As mentioned above, the `--preset chip` argument of `chromap` includes the removal of duplicates (`--remove-pcr-duplicates` set by the preset) and thus, the downstream `PRESEQ_LCEXTRAP` process fails …
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Dear Prof. Dozmorov,
Thanks for your collection of single cell ATAC tools and papers! This is such a cool collection.
Here I'd like to share some of the works from me and Dr. Junhyong Kim on s…
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Hello,
I have been trying to integrate my multiome object and my scATAC-seq data from 10X genomics. The multiome has already been analyzed so I was just trying to merge the multiome with scATAC d…
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**Describe the bug**
Dear Ryan and Jeff, I was running into a problem with the projectBulkATAC function (which I find really useful!!).
I use the recent version from githuub and commented out
.…
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I'm analysing the paired RNA-seq and ATAC-seq data according to the [tutorial].(https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html)
I get the "The 2 combined objects have n…
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Hi,
I would like to use MACS2 for ATAC-seq. Could you please explain the reasoning behind the default value for max-gap being the detected read length (= tag size). Since tags are extended anyway, …
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Dear @timoast,
I encountered an error message of "Error: non-conformable matrix dimensions in dimCheck(e1, e2)" while running GeneActivity to obtain the counts matrix. I followed the Vignette (https:…
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when I used the script of fig5C(data = tibble(value = value[-c(1:2)],time =time)
model = loess(value ~ time, data)), I had a error like:
Error in simpleLoess(y, x, w, span, degree = degree, parametr…
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hey sir,i meet a problem.when i run the **caper init local**,it shows this misitake.
i use the conda
caper init local
/home/zjin/anaconda3/envs/encode-atac-seq-pipeline/lib/python3.6/site-packag…