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[csei]: ../images/csei_examples.png | ||
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###Synopsis | ||
The `cis-splice-effects associate` command is used to identify splicing misregulation events. This command is similar to `cis-splice-effects identify`, but takes the BED output of `junctions extract` in lieu of a BAM file with RNA alignments. The tool then proceeds to associate non-canonical splicing junctions near the variant sites. | ||
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###Usage | ||
`regtools cis-splice-effects associate [options] variants.vcf junctions.bed ref.fa annotations.gtf` | ||
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###Input | ||
| Input | Description | | ||
| ------ | ----------- | | ||
| variants.vcf | Variant call in VCF format from which to look for cis-splice-effects.| | ||
| junctions.bed | BED file of junctions to look through for evidence of splice events. The file is expected to be in the [BED12 format](junctions-extract.md#output) of the `junctions extract` output. | | ||
| ref.fa | The reference FASTA file. The donor and acceptor sequences used in the "splice-site" column of the annotated junctions are extracted from the FASTA file. | | ||
| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions and variants. For examples, the Ensembl GTFs for release78 are [here](ftp://ftp.ensembl.org/pub/release-78/gtf/).| | ||
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**Note** - Please make sure that the version of the annotation GTF that you use corresponds with the version of the assembly build (ref.fa) and that the co-ordinates in the VCF file are also from the same build. | ||
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###Options | ||
| Option | Description | | ||
| ------ | ----------- | | ||
| -o STR | Output file containing the aberrant splice junctions with annotations. [STDOUT] | | ||
| -v STR | Output file containing variants annotated as splice relevant (VCF format). | | ||
| -j STR | Output file containing the aberrant junctions in BED12 format. | | ||
| -s INT | Strand specificity of RNA library preparation, where 0 = unstranded/XS, 1 = first-strand/RF, 2 = second-strand/FR. This option is required. If your alignments contain XS tags, these will be used in the "unstranded" mode. | | ||
| -w INT | Window size in b.p to associate splicing events in. The tool identifies events in variant.start +/- w basepairs. Default behaviour is to look at the window between previous and next exons. | | ||
| -e INT | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in exonic space, i.e a coding variant. [3] | | ||
| -i INT | Maximum distance from the start/end of an exon to annotate a variant as relevant to splicing, the variant is in intronic space. [2] | | ||
| -I | Annotate variants in intronic space within a transcript(not to be used with -i). | | ||
| -E | Annotate variants in exonic space within a transcript(not to be used with -e). | | ||
| -S | Don't skip single exon transcripts. | | ||
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###Output | ||
For an explanation of the annotated junctions that are identified by this command please refer to the output of the `junctions annotate` command [here](junctions-annotate.md#output) | ||
For an explanation of the annotated variants that are identified by this command when using the -v option, please refer to the output of the `variants annotate` command [here](variants-annotate.md#output) | ||
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###Examples | ||
![cis-splice-effects identify example][csei] |
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