Sakura

Hi @cflerin , I truly appreciate your answer. I may misunderstand but the latest version is 0.11.2, right? Did you mean that that issue is unable to resolve until the...

Hi @cflerin, Thank you very much for your quick response. Zebrafish gene names (symbols) are consist of both upper and lower cases. For example, ABR (ENSDARG00000059587; Chr5:62374092-62545913), abr (ENSDARG00000095180; Chr5:62611400-62642718)...

Hi @Igor0411 > I found a solution for my case, maybe it will be helpfull for someone else. I had errors with kallisto-bustools generated loom file. But with velocyto generated...

> Hi @stanaka6 I wasn't able to read kallisto-bustools generated loom file in any R package. As it said in the error this file lack some vital information. So, I...

Hi, Thank you so much for your quick reply. I was able to get the sequences as a fast file. Then I ran `create_cistarget_motif_databases.py`. However, I got the following error:...

Thank you so much for your reply. Here are the outputs: ``` file "updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa" updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa: ASCII text ``` ``` file "Numbered_updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa" Numbered_updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa: ASCII text ``` ``` grep -m 10 '^>'...

FASTA files are available from [here](https://umbc.box.com/s/iyec3eafq0sbhwtrpu8atrlfcpxqbhpe). ``` grep '^>$' "updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa" ``` The output is lines with only ">" (135 lines). ``` grep '^>$' "Numbered_updown10k-5UTR_zf_GRCz11_genesymbol_biomart_nonunique_0804233944_128.fa" ``` The output is a line...

Hi, I was able to run create_cistarget_motif_databases.py using the cleaned FASTA file you explained above. Thank you so much for your help. I checked one of the feather files in...

Hi, Please ignore my last question1. I didn't check the entire data, and there is no conversion for lower and upper cases. My bad, sorry.