So I am just trying to sort a bed file in the following way:
sort-bed GSE63137_ATAC-seq_PV_neurons_HOMER_peaks.bed > GSE63137_ATAC-seq_PV_neurons_HOMER_peaks_sorted.bed
It is only a 3 column bed file:
chrY 90810610 90811697 chrY 90812379 90813359 chrY 90828628 90829131 chrY 90838917 90839418
I am getting the following error, and that last line you see is whats causing it seems, thanks!
File has never been opened in excel.
No end of line found at 103361 in GSE63137_ATAC-seq_PV_neurons_HOMER_peaks.bed. May need to increase BED_LINE_LEN and recompile. First check that you have unix newlines (cat -A).