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If you search with Glycan Motif ID - GGM.000001 on super search you get 173 associated proteins but if you see on the No of proteins on motif list (https://www.glygen.org/list-of-motifs/) for GGM.0000…
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**User story**
As a developer I need to reduce the technical debt for pacbio runs as it is not setup correctly which is causing hidden bugs and issues. It is also not tested thoroughly or correctly i…
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`make amino_report` generates incorrect results for every amino acid. Would be a good idea to go ahead with the new percentage-based amino similarities after all.
This affects the best-binding algo…
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Hi! First and foremost, thank you for developing and maintaining such an amazing tool.
I have used TOBIAS to make a simple comparison between control cells and knockdown cells for two proteins. I hav…
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Hi! I have a zebrafish dataset (ref genome: danRer11) and I am starting to run CellOracle.
In the '**transcription factor binding motif scan**', I have reached to '**3. Instantiate TFinfo object …
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Hello,
Do you have a specific recommended protocol for amplifying ssDNA MIPs designed through MIPGen? For example specific polymerase, ng of input, number of cycles? Your supplemental states "8. PCR a…
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**Describe the bug**
Hi! I tried to reproduce the tutorial regarding the mouse brain data set (http://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/SCENIC%20…
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Hello,
I'm running BINDetect using the following input:
TOBIAS BINDetect --motifs ${PFM} --signals */*_footprints.bw --genome ${GENOME} --peaks tmp.clip.bed --peak_header peak_header.txt --outdir …
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https://mp.weixin.qq.com/s/4IAXMbijZ6YEqh8yj9n0Ig
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Hi,
I have what might be a basic question. What's the difference between the "all" vs "bound" files? Does "all" mean all the motif occurrences in the open chromatin peaks, and "bound" means the mot…