Hi everyone,
I am trying to do bedtools coverage with my .bed and .bam files; however, only half of the .bed files worked, while the other half had this error:
Error: unable to open file or unable to determine types for file SRR14194209_minus_bottom_sorted_removed_opposite_gene_6kb.bed
- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED).
When I checked for tab delimited, cat -t FILE
, here was the output example for all the files:
chr4^I119280127^I119286127^IID=FL_L1-1635^I.^I-^I119274114^I119280127^IL1.3_300bp5NoF^I6^I593^I6013^I0.0986197
Any insights of what might be happening? Thank you so much in advance!
what is the output of the following commands:
Here is the output:
the output of the
file
command is missing;Yes, so sorry, my bad. Here is the output: