About bedtools closest command line output understanding

Question

[bk11]

Hi, I used bedtools command to get nearest expressed genes and long non coding RNA and got result like this. I really did not understand the last column. Why distance is not matching?

Command used:

bedtools closest -a lincRNA.gtf -b *_lincRNAs.bed -d | head | less -S

Output:

1  432600  433992  ENSGALG00000036347  lincRNA +       1       1       531144  532064  .       .       +       Cufflinks       exon    .       gene_id "XLOC_000013"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS13";        97153

[Alex Reynolds]

Possible alternative: http://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html

[James Ashmore]

Can you post a snippet of your GTF and BED files?

[bk11]

Hello James Ashmore,
Here are the snippets:
GTF:
1       432600  433992  ENSGALG00000036347      lincRNA +
1       698664  700562  ENSGALG00000033552      lincRNA +
1       754797  757791  ENSGALG00000034779      lincRNA +
1       787776  789085  ENSGALG00000034602      lincRNA +
1       1014153 1015081 ENSGALG00000043038      lincRNA +
1       1016111 1018736 ENSGALG00000008153      lincRNA +
1       1161094 1189206 ENSGALG00000042593      lincRNA -
1       1355907 1356649 ENSGALG00000039622      lincRNA +

BED:
1       531144  532064  .       .       +       Cufflinks       exon    .       gene_id "XLOC_000013"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS13";
1       745809  746104  .       .       -       Cufflinks       exon    .       gene_id "XLOC_002014"; transcript_id "TCONS_00002492"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS2192";
1       755070  755280  .       .       -       Cufflinks       exon    .       gene_id "XLOC_002016"; transcript_id "TCONS_00002494"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS2194";
1       1304961 1305339 .       .       -       Cufflinks       exon    .       gene_id "XLOC_002040"; transcript_id "TCONS_00002519"; exon_number "1"; oId "CUFF.50.1"; class_code "u"; tss_id "TSS2218";
1       1305924 1306186 .       .       -       Cufflinks       exon    .       gene_id "XLOC_002041"; transcript_id "TCONS_00002520"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS2219";
1       3031193 3031408 .       .       +       Cufflinks       exon    .       gene_id "XLOC_000057"; transcript_id "TCONS_00000070"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS62";
1       3034131 3034340 .       .       +       Cufflinks       exon    .       gene_id "XLOC_000058"; transcript_id "TCONS_00000071"; exon_number "1"; oId "CUFF.60.1"; class_code "u"; tss_id "TSS63";
1       3034902 3035641 .       .       -       Cufflinks       exon    .       gene_id "XLOC_002049"; transcript_id "TCONS_00002531"; exon_number "1"; oId "CUFF.61.1"; class_code "u"; tss_id "TSS2228";