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Hi,
I've established a link to the FTS API interface and I can insert (POST) entities and then use ManageGeoObject/getGeoObject to retrieve them from the server. Also, when I add them using the API I…
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I am trying to call peaks in ATAC-seq data. According to the documentation:
> To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5' ends of sequenced reads should be ex…
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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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**Describe the bug**
It seems that the MD tag generated in Chromap sometimes can incorrectly begin with a letter. It seems this behavior, to my understanding occurs when the first character is a 0. Mo…
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hello,
Thank you for this package! Is there a way to extract the original cells for both the RNA and ATAC-seq that were used to make the pseudomultiome and map those to the cells for the output mat…
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Hi,
Could you maybe add an explanation of what exactly the ATACseq mode (-A flag) is doing differently to DNase mode? Also should the input BAMs for ATACseq mode be Tn5 shifted or not?
Thanks
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Hello,
Thanks for this very useful package!
I just have a few questions after runnning on single-cell ATAC-Seq libraries generated from the 10X multiome kit. I ran using the following commands:
…
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When I attempt trimodal rna-atac-adt or bimodal atac-adt integration, `MultiMAP.Integration` fails with the error:
`---------------------------------------------------------------------------
ValueE…
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The main challenge with using this pipeline for ATAC-seq data is the use of STAR for mapping within the WASP subworkflow. We could create two new mapping rules within the WASP subworkflow that use `bo…