Bedtools Intersect with files containing some alternative information

Question

[christylynn002]

Do two files have to have the exact same information in them to intersect the two files? I'm trying to intersect these two files with a format similar to below:

Example of file 1:

chrom   exon_start      exon_end        strand  isoform exon_numer      gene    coding_length   total_mutations_reported        total_exonic_mutations  exonic_splicing_mutations       total_splice_site_mutations     3_ss_mutations  5_ss_mutations
chr17   7125985 7126184 +       NM_000018       10      ACADVL  199     15      11      0       4       2       2
chr17   7126962 7127049 +       NM_000018       12      ACADVL  87      7       4       0       3       1       2
chr11   108016928       108017086       +       NM_000019       11      ACAT1   158     10      7       1       3       2       1
chr12   52307342        52307554        +       NM_000020       4       ACVRL1  212     10      7       0       3       1       2

Example of file 2:

chr1    957580  957842  NM_198576       2       +       AGRN    262     0       0       0       0       0       0       exon    GTTCGGGTCTGGCGGTACTTGAAGGGCAAAGACCTGGTGGCCCGGGAGAGCCTGCTGGACGGCGGCAACAAGGTGGTGATCAGCGGCTTTGGAGACCCCCTCATCTGTGACAACCAGGTGTCCACTGGGGACACCAGGATCTTCTTTGTGAACCCTGCACCCCCATACCTGTGGCCAGCCCACAAGAACGAGCTGATGCTCAACTCCAGCCTCATGCGGATCACCCTGCGGAACCTGGAGGAGGTGGAGTTCTGTGTGGAAG  0.72692929292929
chr1    989132  989357  NM_198576       34      +       AGRN    225     0       0       0       0       0       0       exon    CGAGAAGGCACTGCAGAGCAACCACTTTGAACTGAGCCTGCGCACTGAGGCCACGCAGGGGCTGGTGCTCTGGAGTGGCAAGGCCACGGAGCGGGCAGACTATGTGGCACTGGCCATTGTGGACGGGCACCTGCAACTGAGCTACAACCTGGGCTCCCAGCCCGTGGTGCTGCGTTCCACCGTGCCCGTCAACACCAACCGCTGGTTGCGGGTCGTGGCACATAG       0.72252380952381

I want my output of intersect to be the information from file one. However, when I try bedtools intersect -a file1.bed -b file2.bed -wa I get this Error: unable to open file or unable to determine types for file total_splice_site_mut_greater3.bed. I just want to compare the first three columns of my files for returns, but I'm assuming that's not possible with bedtools if the files don't contain the same information. Am I correct? Any ideas on how I can achieve my desired result?

Edit: total_splice_sit_mut_greater3.bed is file1.bed

[raunakms]

your file1 doesn't seem to follow proper BED file format.

Answer 1

[Ram]

File1.bed has a header where cols 2 and 3 are not numeric. Try extracting tail -n +2 of File1.bed to a File1_beheaded.bed and then running bedtools.

[christylynn002]

Thank you. I should have noticed that.