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So it is important to know which version of BEDTools you are using, and read the documentation carefully to see if changes have been made since your version. When you run the code below, you should see that the version on TACC is bedtools v2.25.0. (Login to login5.ls5.tacc.utexas.edu first.)
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module load bedtools bedtools --version |
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Take a quick look at a yeast annotation file, sacCer_R64-1-1_20110208.gff using less. (Login to login5.ls5.tacc.utexas.edu first.)
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mkdir -p $SCRATCH/core_ngs/bedtools cd $SCRATCH/core_ngs/bedtools cp $CORENGS/yeast_rna/sacCer_R64-1-1_20110208.gff . less sacCer_R64-1-1_20110208.gff |
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You should see something like this.
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7077 CDS
6607 gene
480 noncoding_exon
383 long_terminal_repeat
376 intron
337 ARS
299 tRNA
190 region
129 repeat_region
102 nucleotide_match
89 transposable_element_gene
77 snoRNA
50 LTR_retrotransposon
32 telomere
31 binding_site
27 rRNA
24 five_prime_UTR_intron
21 pseudogene
17 chromosome
16 centromere
15 ncRNA
8 external_transcribed_spacer_region
8 internal_transcribed_spacer_region
6 snRNA
3 gene_cassette
2 insertion |
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The program reads the input file twice – once to gather all the attribute names, and then a second time to write the attribute values in well-defined columns. You'll see output like this:
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---------------------------------------- Gathering all attribute names for GTF 'sc_genes.gff'... urlDecode = 1, tagAttr = tag Done! 6607 lines read 6607 locus entries 8 attributes found: (Alias ID Name Note Ontology_term dbxref gene orf_classification) ---------------------------------------- Writing BED output for GTF 'sc_genes.gff'... Done! Wrote 6607 locus entries from 6607 lines |
To find out what the resulting columns are, look at the header line out the output BED file:
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head -1 sc_genes.converted.bed |
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Doesn't this look better?
| Code Block | title | Converted BED attributes
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chrI 334 649 YAL069W 315 + YAL069W Dubious chrI 537 792 YAL068W-A 255 + YAL068W-A Dubious chrI 1806 2169 YAL068C 363 - PAU8 Verified chrI 2479 2707 YAL067W-A 228 + YAL067W-A Uncharacterized chrI 7234 9016 YAL067C 1782 - SEO1 Verified chrI 10090 10399 YAL066W 309 + YAL066W Dubious chrI 11564 11951 YAL065C 387 - YAL065C Uncharacterized chrI 12045 12426 YAL064W-B 381 + YAL064W-B Uncharacterized chrI 13362 13743 YAL064C-A 381 - YAL064C-A Uncharacterized chrI 21565 21850 YAL064W 285 + YAL064W Verified chrI 22394 22685 YAL063C-A 291 - YAL063C-A Uncharacterized chrI 23999 27968 YAL063C 3969 - FLO9 Verified chrI 31566 32940 YAL062W 1374 + GDH3 Verified chrI 33447 34701 YAL061W 1254 + BDH2 Uncharacterized chrI 35154 36303 YAL060W 1149 + BDH1 Verified chrI 36495 36918 YAL059C-A 423 - YAL059C-A Dubious chrI 36508 37147 YAL059W 639 + ECM1 Verified chrI 37463 38972 YAL058W 1509 + CNE1 Verified chrI 38695 39046 YAL056C-A 351 - YAL056C-A Dubious chrI 39258 41901 YAL056W 2643 + GPB2 Verified |
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