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Copy file name to clipboardExpand all lines: docs/commands/junctions-annotate.md
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@@ -17,7 +17,7 @@ Gene Annotation databases such as Ensembl/RefSeq/UCSC etc. The goal of the annot
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| junctions.bed | The BED file with the junctions that have be annotated. This file has to be in the BED12 format. One recommended way of obtaining this file is by running `regtools junctions extract`. See [here](junctions-extract.md) for more details.|
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| ref.fa | The reference FASTA file. The donor and acceptor sequences used in the "splice-site" column are extracted from the FASTA file. |
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| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions. For examples, the Ensembl GTFs for release78 are [here](ftp://ftp.ensembl.org/pub/release-78/gtf/)|
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| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions. For examples, the Ensembl GTFs for release 106 are [here](http://ftp.ensembl.org/pub/release-106/gtf/).||
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