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clean doc
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Juke34 committed Apr 15, 2021
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2 changes: 1 addition & 1 deletion docs/gff_to_bed.md
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Expand Up @@ -18,7 +18,7 @@ to perform the conversion. We will try to see in this review the main difference
## Test summary

tool | Comment
-- | -- |
-- | --
[AGAT](https://github.com/NBISweden/AGAT) | default RGB color to 255,0,0
[PASA](https://github.com/PASApipeline/PASApipeline) | Particular 3rd column that contains a list of names
[bedops](https://github.com/bedops/bedops) | each gff feature give one line. Only the 6 first colums are correct
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2 changes: 1 addition & 1 deletion docs/gff_to_gtf.md
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## Test summary

tool | respect GTF format | UTR conserved | attribute conserved | Stop codon removed from CDS | Comment
-- | -- | -- | -- | -- | -- |
-- | -- | -- | -- | -- | --
[AGAT](https://github.com/NBISweden/AGAT) | Yes - All (default GTF3) | Yes it converts UTR terms to the appropriate ones according to the GTF version selected.| Yes - All | Yes | Can take any GTF GFF as input. The only one keeping comments at the beginning of the file.
[gffread](https://github.com/gpertea/gffread) | No - They say GTF2.2 but it is not: transcript should be removed; start_codon and stop_codon should stay. | No | No | No
[GenomeTools](https://github.com/genometools/genometools) | No - only CDS and exon kept | No | No | No | gene_id and transcript_id get new identifiers.
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2 changes: 1 addition & 1 deletion docs/gxf.md
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Expand Up @@ -402,7 +402,7 @@ Originally Ensembl has created the GTF format that has been then slightly modifi
## Resume

### Timeline of the different formats
<img align="center" src="pictures/gff_history.jpg"/>
<img align="center" src="gff_history.jpg"/>

### Main points and differences between GFF formats

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