How can I convert GFF3 to GFF file using rtracklayer package?

Question

[gustavoborin01]

Hi everyone. I'm trying to convert a GFF3 annotation file to GFF format, using the command lines below on rtracklayer package, but I'm not successfull. Does anyone could help me with this? I'm new on R.

annotation_path <- system.file("annotation", package = "rtracklayer")
annotation_gff3 <- file.path(test_path, "TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gff3")
test <- import(annotation_gff3)
export(test,"annotation.gtf","gtf")

Thanks a lot!

Gustavo P.

[gustavoborin01]

I've tried this, but I can't find any GFF output file. I have to set a directory for the output file? Sorry about my inexperience. I'm a master student and I'm trying to convert this file to use as a object in the rsubread package.

> annotation<- import("TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gff3")
> annotation
GRanges with 76358 ranges and 7 metadata columns:
                           seqnames         ranges strand   |   source
                              <Rle>      <IRanges>  <Rle>   | <factor>
      [1] TrireRUTC30_1_scaffold_23 [44782, 45986]      -   |      JGI
      [2] TrireRUTC30_1_scaffold_23 [44782, 45986]      -   |      JGI
      [3] TrireRUTC30_1_scaffold_23 [44782, 45549]      -   |      JGI
      [4] TrireRUTC30_1_scaffold_23 [45634, 45819]      -   |      JGI
      [5] TrireRUTC30_1_scaffold_23 [45921, 45986]      -   |      JGI
      ...                       ...            ...    ... ...      ...
  [76354] TrireRUTC30_1_scaffold_47 [22225, 23399]      -   |      JGI
  [76355] TrireRUTC30_1_scaffold_47 [22225, 23275]      -   |      JGI
  [76356] TrireRUTC30_1_scaffold_47 [23359, 23399]      -   |      JGI
  [76357] TrireRUTC30_1_scaffold_47 [22225, 23275]      -   |      JGI
  [76358] TrireRUTC30_1_scaffold_47 [23359, 23399]      -   |      JGI
              type     score     phase                      ID
          <factor> <numeric> <integer>             <character>
      [1]     gene      <NA>      <NA>           e_gw1.23.89.1
      [2]     mRNA      <NA>      <NA>         e_gw1.23.89.1-T
      [3]     exon      <NA>      <NA>      e_gw1.23.89.1-T-E1
      [4]     exon      <NA>      <NA>      e_gw1.23.89.1-T-E2
      [5]     exon      <NA>      <NA>      e_gw1.23.89.1-T-E3
      ...      ...       ...       ...                     ...
  [76354]     mRNA      <NA>      <NA>    fgenesh1_pg.47_#_6-T
  [76355]     exon      <NA>      <NA> fgenesh1_pg.47_#_6-T-E1
  [76356]     exon      <NA>      <NA> fgenesh1_pg.47_#_6-T-E2
  [76357]      CDS      <NA>         1  fgenesh1_pg.47_#_6-T-P
  [76358]      CDS      <NA>         0  fgenesh1_pg.47_#_6-T-P
                        Name               Parent
                 <character>      <CharacterList>
      [1]      e_gw1.23.89.1                     
      [2]      e_gw1.23.89.1        e_gw1.23.89.1
      [3]               <NA>      e_gw1.23.89.1-T
      [4]               <NA>      e_gw1.23.89.1-T
      [5]               <NA>      e_gw1.23.89.1-T
      ...                ...                  ...
  [76354] fgenesh1_pg.47_#_6   fgenesh1_pg.47_#_6
  [76355]               <NA> fgenesh1_pg.47_#_6-T
  [76356]               <NA> fgenesh1_pg.47_#_6-T
  [76357]               <NA> fgenesh1_pg.47_#_6-T
  [76358]               <NA> fgenesh1_pg.47_#_6-T
  ---
  seqlengths:
    TrireRUTC30_1_scaffold_23 ...  TrireRUTC30_1_scaffold_47
                           NA ...                         NA
> export.gff2(annotation, "TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gff3")

[Michael]

but I can't find any GFF output file. I have to set a directory for the output file?

No, the files will be created in your working directory, but you are using the same filename of the input file and therby overwriting it:

export.gff2(annotation, "TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gff3")
                                                                      ^___^

should it be .gff2?

Answer 1

[Michael]

Try export.gff2

[gustavoborin01]

Thanks Michael for help me! I have tried to do what you said me, but it didn't work. So, I try to use the gffread function from cufflinks package and finally it worked. For who wants to convert GFF3 to GTF, I recommend using the command line below:

gffread my.gff3 -T -o my.gtf