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Hi,
Is there limit on the maximum motif size that EHDN can detect repeats for?
The EHDN runs for all my samples (250*2 bp PE WGS data) saw a maximum of 20 based motifs. If there is, then can I incre…
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Meeting note on Feb 26. 2021
1. DNA footprinting pipeline(shared by Shannon): http://www.regulatory-genomics.org/hint/introduction/
2. DNA footprinting paper (shared by Shannon): https://genomebiolo…
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Hello!
I have very little coding experience, and I was wondering if it was possible to run AptaTrace without the primer regions being involved in structure prediction. My SELEX experiment removed t…
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Hi CellOracle team,
We noticed that the file "TAIR10_tss_info.bed.txt" you provided for Arabidopsis thaliana TAIR10 motif analysis contains gene names that correspond to different genes. For exampl…
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@aarmey during my lab meeting I realized I was trying to solve separate problems with the same solutions whereas they should be addressed individually so I put together this table to summarize what we…
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## Bi-weekly meeting memo
0. Files that Shannon will share to Tao
- ATAC-seq datasets: fastq
- variant dataset: vcf
- packages: R Bioconductor, ChIPPeakAnno, ChipSeerker
1. make the footprint f…
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Hi I am trying to subset the archr obj by extracting cell from a few clusters and running into the below error. When i subset an archr object without motif matrix it subsets fine. But when it has a mo…
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I want to use human_pwms_v2 (https://github.com/GreenleafLab/chromVARmotifs) to do motif analysis. But it is a pwm format. I check the parameter of addMotifs function, it only have a pfm parameter. …
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[Splicing mechanism](https://www.youtube.com/watch?v=vMMt0jA8dcM)
Intron
- starting point: 5' (5 prime) splice site: splice donor, GT***
- ending point: 3' (3 prime) splice site: splice acceptor, *…
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https://mp.weixin.qq.com/s/DxNooI4qu3fr9oAcdT0mRA
ixxmu updated
2 years ago