Ming Tang
hey @jeremymsimon @rob-p I was processing some 10x5' V2 data last week and the number of reads per cell is much fewer than the cellranger output. I then found this...
Hi, The JASPAR motif is in a different format than gimmme accepts. How can I convert it? http://jaspar.genereg.net/download/CORE/JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.txt Thanks! Tommy
@Rmulet thanks for sharing the code!
need to add the new line ```python jaspar_file = "JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.txt" outfile = open("JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.pwm", "w") with open(jaspar_file) as f: motifs = read_motifs(f, fmt="jaspar") # Print them in .pwm format used by...
Hi, I got a key error: ``` gimme maelstrom myinput.txt hg19 maelstrom.JASPAR18.out -p /apps/conda/envs/gimme/share/gimmemotifs/motif_databases/JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.pwm 2018-05-07 23:22:48,410 - INFO - Starting maelstrom 2018-05-07 23:22:48,423 - INFO - Motif scanning (counts) 2018-05-07...
UPDATE. if I did not change the tab to `_`, I got a different error: ```bash gimme maelstrom my_input.txt hg19 maelstrom_JASPAR18.out -p /apps/conda/envs/gimme/share/gimmemotifs/motif_databases/JASPAR2018_CORE_vertebrates_non-redundant_pfms_jaspar.pwm 2018-05-08 08:24:34,970 - INFO - Starting maelstrom...
No problem! in the motif_database folder, there are files gimme.vertebrate.v3.1.motif2factors.txt I need to create one for JASPAR2018 as well?
when one uses different motifs .pwm files, how `gimme maelstrom` finds the correct linking file? I need to give the same prefix for the linking file and the pwm file?
Hi, The FDR for Epic2-df is confusing to me. why there are two FDRs for the same region? if a region is down with an FDR 0.05 comparing KO to...
okay. thanks for answering.