You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/commands/cis-splice-effects-identify.md
+1-1Lines changed: 1 addition & 1 deletion
Display the source diff
Display the rich diff
Original file line number
Diff line number
Diff line change
@@ -15,7 +15,7 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
15
15
| variants.vcf | Variant call in VCF format from which to look for cis-splice-effects.|
16
16
| alignments.bam | Aligned RNAseq BAM/CRAM produced with a splice aware aligner, that has been indexed for example with `samtools index`. We have tested this command with alignments from TopHat.|
17
17
| 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. |
18
-
| 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/).|
18
+
| annotations.gtf | The GTF file specifies the transcriptome that is used to annotate the junctions and variants. For examples, the Ensembl GTFs for release 106 are [here](http://ftp.ensembl.org/pub/release-106/gtf/).|
19
19
20
20
**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.
0 commit comments