Skip to content

Commit

Permalink
Merge pull request #111 from griffithlab/doc_associate
Browse files Browse the repository at this point in the history
strand, associate
  • Loading branch information
yang-yangfeng committed Apr 3, 2019
2 parents 189fd4b + cdfcead commit c296371
Show file tree
Hide file tree
Showing 4 changed files with 41 additions and 2 deletions.
38 changes: 38 additions & 0 deletions docs/commands/cis-splice-effects-associate.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
[csei]: ../images/csei_examples.png

###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.

###Usage
`regtools cis-splice-effects associate [options] variants.vcf junctions.bed ref.fa annotations.gtf`

###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/).|

**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.

###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. |

###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)

###Examples
![cis-splice-effects identify example][csei]
2 changes: 1 addition & 1 deletion docs/commands/cis-splice-effects-identify.md
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
| -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 (0 = unstranded, 1 = first-strand/RF, 2, = second-strand/FR). [1] |
| -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 identify 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] |
Expand Down
1 change: 1 addition & 0 deletions docs/commands/commands.md
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ This set of tools helps identify and work with aberrant splicing events near var
Below are links to detailed explanations of the `cis-splice-effects` sub-commands:

- [identify](cis-splice-effects-identify.md)
- [associate](cis-splice-effects-associate.md)

##cis-ase
This set of tools helps identify and work with allele-specific-expression near variants, these could be somatic variants or germline polymorphisms/mutations. These variants are hypothesized to act in cis and affect how the gene is transcribed.
Expand Down
2 changes: 1 addition & 1 deletion docs/commands/junctions-extract.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ The `junctions extract` command can be used to extract exon-exon junctions from
| -o | File to write output to. STDOUT by default.|
| -r | Region to extract junctions in. This is specified in the format "chr:start-end". If not specified, junctions are extracted from the entire BAM file.|
| -h | Display help message for this command.|
| -s | Strand specificity of RNA library preparation, where 0 = unstranded, 1 = first-strand/RF, 2 = second-strand/FR. The default is 1 (RF). This option is meant to be used if no XS tags are present in the input BAM.
| -s | 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.

###Output
The output is in the BED12 format which is described in detail [here.](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) Each line is an exon-exon junction as explained below.
Expand Down

0 comments on commit c296371

Please sign in to comment.