Closed BokaiZhu closed 2 years ago
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The file in question looks corrupted in some way. When I download that file and try to unzip it or use zcat to read the lines, it does not contain a standard text file. I would contact the authors of that paper if you see the same thing and need further assistance with their files.
Thanks! Contacted the authors.
Hi ArchR team, thanks for providing this wonderful tool for atac data!
I have run through the tutorial, and was able to read in the fragment files via function
createArrowFiles
with the tutorial fragments. However, when I was trying to read in some other fragment files (the ones from "Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci" under GSE165860, the reading failed where nothing was loaded.The code used here (where I tried loading with Hg38 as specified in the paper):
The message I got:
and the
ArrowFiles1
was empty, unlike when reading the files provided in the tutorial.I also made couple tests on the files under the same GSE deposition series, seems I wasn't able to read any of them, so likely not a truncated download problem.
I also tried fragment files from the other ArchR paper (nature genetics, GSE162690), and the reading was good (using hg19 in that case).
I also checked other fragment files aligned with hg38 in another paper: GSE139369. Files read in without any problem.
I checked changing the thread to 1, or chaning nchunk to 1, and the problem still persists.
the log file is as: ArchR-createArrows-94133f6837ed-Date-2022-02-10_Time-23-46-13.log
Please let me know what part I got wrong and thanks for the help in advance! Withe these testing I'm thinking if the fragment files under GSE165860 need different parameters?