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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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[results]about MotifSimilarityQvalue, OrthologousIdentity and Annotation in results #587

Open SYSUMSD opened 1 month ago

SYSUMSD commented 1 month ago

Hi, I have created a chicken TF reference database and completed the pySCENIC analysis in my chicken data. But I find a problem in my result from pyscenic ctx program output file:

微信图片_20241017174536 This is the result of TF ABL1, and it shows that this TF has 100+ motifs without MotifSimilarityQvalue, OrthologousIdentity and Annotation information.

But when I check this gene in motifs-v10-nr.chicken-m0.00001-o0.0.tbl witch is downloaded from https://resources.aertslab.org/cistarget/motif_collections/v10nr_clust_public/snapshots/ , this gene only has 1 record:

transfac_pro__M08187 M08187 V$ABL1_01: ABL1 transfac_pro 2021.2 ABL1 0.0 NaN NaN 0.823582 ENSG00000097007 H. sapiens gene is orthologous to ENSG00000097007 in H. s...

This record showes this gene has only 1 motif. Why are there more motifs annoted by pyscenic ctx program than tbl file?

My chicke TF database is created using motif information from (https://resources.aertslab.org/cistarget/motif_collections/v10nr_clust_public/singletons/)

SYSUMSD commented 1 month ago

The second problem is why dose the records from pyscenic ctx program have the records without MotifSimilarityQvalue, OrthologousIdentity and Annotation information? How were these records created?