Gert Hulselmans
Gert Hulselmans
@LILI-0000-0002-8173-7367 Are you sure that you installed the latest git version (and not only pulled it)?
Latest pySCENIC git version should fix this numpy issue now: https://github.com/aertslab/pySCENIC/commit/31d51a1625f12fb3c6e92bc48ecc9d401524c22a
The size of the feather files depends on the number of motifs used multiplied by the number of genes/regions used multiplied by 2 or 4 bytes (depending if number of...
In human and mouse we have 27k and 24k genes respectively and 24k motifs: ``` hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather: 1327758248 bytes 27165 genes * 24324 motifs * 2 bytes = 1321522920 bytes (for...
> writing to disk of `*.tracks_vs_regions.rankings.feather` is commented out, so I guess we don't need this file, right? No, this file does not need to be saved. It is only...
@eboileau What was the full command that you ran? I suspect that your input feather file you used was not in the proper format. ``` Traceback (most recent call last):...
Thanks for providing the test files. In case you would need to run 1`convert_motifs_or_tracks_vs_regions_or_genes_scores_to_rankings_cistarget_dbs.py` in the future, the bug is fixed (missing 1 character): https://github.com/aertslab/create_cisTarget_databases/commit/9572f4147bcd9853571a687a2b3833241bff641d#diff-09ae4856d6de6fde66c2e4398454f6d41a333c12d018f20b0f0969b2f5b95cffR508
> Ok, so now I have my *regions_vs_tracks.rankings.feather to run pySCENIC. What about the difference between "regions" or "genes", i.e. more in terms of overall performance, do you have any...
A number of years ago we tried to make a database for Zebrafish (assembly: GRCz10). At the time the test (ChIP-seq) datasets (top 500 regions from ChIP-seq) we had didn't...
At first glans it looks like your have lines which start with `>` without identifier. Can you post the output of the following commands: ``` # Output of: file "updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa"...