Closed ddb-qiwang closed 3 years ago
I meet the same problem. Can the authors share their "gtf" file suitable for the "episcanpy.tl.geneactivity"?
Hi,
Very sorry for this delayed answer! So far we have been using gif files from gencode so I don't really know where this error is coming from. But I am looking into it.
In the meantime, here is the mouse genome annotation I have been using: https://www.dropbox.com/s/2h1naiiigocacs2/gencode.vM23.primary_assembly.annotation.gtf?dl=0 Here is the human genome annotation I just tested: https://www.dropbox.com/s/jfj5bhqm28t7imb/gencode.v36.annotation.gtf?dl=0
Hi,
Is this because the data file is compressed? I found the same error in StackOverflow.
Hello! When I use function 'episcanpy.tl.geneactivity' to collapse the peak matrix to a "gene activity matrix", I met ‘UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte’ at 'with open(gtf_file) as f: for line in f:' The gtf file I use is gzip file 'hg38', acquired from 'genome.ucsc.edu'.