I am trying to prepare my peak file for MEME_chip analysis, but I got an error when using Bedtools Slopbed saying:
Unexpected file format. Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?
I tried inputting a tabular file for the peaks, but it wasn’t allowed to, so I used a bed file instead, but I still got this error. I used a the drosophila genome file dmel-all-r6.43.txt recently downloaded from flybase. Why am I getting this error?
Please check if your file contains a headerline, which you have to remove. I assume it does. You can remove it with the tool “Remove beginning of a file”. If that does not do the trick, then perhaps you do not have a tab-delimited table and Galaxy will show you, that the file only has one column if you inspected it. In that case, you can reformat the file with " Replace Text in entire line" replacing a space " " with a tab “\t”; or just reformatting it into a table/bed file might help.