Hi, I am using bedtools intersect to overlap sites with given data 'REDIportal_Human_AG_all_hg38.bed'.
But when I use code
bedtools intersect -wa -a TTTTGTTGTTGA_call1.out -b REDIportal_Human_AG_all_hg38.bed > TTTTGTTGTTGA_call1_overlap.out
it warning
***** WARNING: File AAACTTGCCCGT_call1.out has inconsistent naming convention for record:
GL000205.2 60017 60018 variant 6.760821593887299 . 5,0,0,0 0,0,5,0 *
***** WARNING: File AAACTTGCCCGT_call1.out has inconsistent naming convention for record:
GL000205.2 60017 60018 variant 6.760821593887299 . 5,0,0,0 0,0,5,0 *
It seems that there were conflicting nomenclature.
The following is the head of file 'AAACTTGCCCGT_call1.out'
contig start end name stat strand bases11 bases21 info
Hi, I am using bedtools intersect to overlap sites with given data 'REDIportal_Human_AG_all_hg38.bed'. But when I use code
bedtools intersect -wa -a TTTTGTTGTTGA_call1.out -b REDIportal_Human_AG_all_hg38.bed > TTTTGTTGTTGA_call1_overlap.out
it warningIt seems that there were conflicting nomenclature.
The following is the head of file 'AAACTTGCCCGT_call1.out'
contig start end name stat strand bases11 bases21 info
chr1 7984947 7984948 variant 0.6603734830715382 . 0,0,6,0 1,0,5,0 chr1 7985096 7985097 variant 0.6220354087561191 . 0,0,9,0 0,1,8,0 chr1 8868047 8868048 variant 0.661881276993924 . 0,6,0,0 0,5,0,1 chr1 8871901 8871902 variant 0.5617532856704202 . 0,0,0,16 1,0,0,15
and the head of file 'REDIportal_Human_AG_all_hg38.bed' chr1 10186 10187 NONE,DDX11L1 0 + chr1 10192 10193 NONE,DDX11L1 0 + chr1 10210 10211 NONE,DDX11L1 0 + chr1 10216 10217 NONE,DDX11L1 0 + chr1 10222 10223 NONE,DDX11L1 0 + chr1 10228 10229 NONE,DDX11L1 0 + chr1 10235 10236 NONE,DDX11L1 0 + chr1 10241 10242 NONE,DDX11L1 0 + chr1 10248 10249 NONE,DDX11L1 0 + chr1 10254 10255 NONE,DDX11L1 0 + chr1 136167 136168 AL627309.1 0 - chr1 136175 136176 AL627309.1 0 -
How shoud I modify the code or the input file? Thank you for answering. Best wishes!