I keep receiving the error when running reformatFragmentReads() for ArchR:
Detected 1 column names bu the data has 5 columns. Added 4 extra default column names at the end.
How would you fix this? For reference, I am working with .tsv.gz files.
Here's the error I face:
EDIT on 15-Jun-2022
I have been having the same error pop up for the past 5 days and have not found any helpful solution to this. Currently I am simply passing a function
reformatFragmentFiles("fragments.tsv.gz"), and I only receive the following message:
Column 1 is length 1283934 which differs from length of column 1 (0).
Can someone provide *helpful solutions to mitigate this issue? Is there a certain manipulation I need to pass on the file directly?
check your input file delimiter....
so the question is "does this software works with gz files... ?"
The software works with .gz files; I've also tried .tsv.gz, .tsv.gz.tbi, etc. It seems to be a formatting issue from the CellRanger derived fragment files unfortunately. And when I try to use the reformatFragmentReads(), I run into the same issue.
I alread did. I'm seeking solutions however (i.e. script for mitigating the issue)...
zgrep first few lines and check the separator. Separator must be in line with program supported separators.
That command is only used to search for patterns; that would not fix the issue.
it's zcat. sorry for the typo. (However you can zgrep
.a gzipped file to print every thing. Don't do it though).
ztailwere builtins similar to
zcat. Aliases can be created, of course, but I'm disappointed at the lack of builtins.
Please copy and paste error messages when possible rather than using screenshots.
Please do not delete posts that have received comments/answers. It is discourteous to people who have tried to help you.
This is also not an acceptable way to create new posts with the same question.