Update index.md

updated test data description
griffithlab · Oct 31, 2023 · c1ba2a2 · c1ba2a2
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commit c1ba2a2
Showing 1 changed file with 3 additions and 20 deletions.
diff --git a/docs/index.md b/docs/index.md
@@ -27,32 +27,15 @@ make
 regtools --help
 ```
 
-If one wishes to test their installation, we include test data under `test_data`.
+If one wishes to test their installation, we include test data under `tests/integration-test/data`.
 
 Here's an example command using that data along with the example output.
 
 ```sh
-regtools cis-splice-effects identify -s RF -e 10 -i 10 test_data/HCC1395_chr22.vcf.gz test_data/HCC1395_tumor.bam test_data/chr22_with_ERCC92.fa test_data/chr22_with_ERCC92.gtf
-
-Variant 22	42129188	42129189	-1
-Variant region is 22:42128784-42130813
+regtools cis-splice-effects identify -s RF tests/integration-test/data/vcf/test1.vcf tests/integration-test/data/bam/test_hcc1395.2.bam tests/integration-test/data/fa/test_chr22.fa tests/integration-test/data/gtf/test_ensemble_chr22.2.gtf
 
 chrom	start	end	name	score	strand	splice_site	acceptors_skipped	exons_skipped	donors_skipped	anchor	known_donor	known_acceptor	known_junction	gene_names	gene_ids	transcripts	variant_info
-position = 22:42125408-42125409
-position = 22:42130565-42130566
-22	42125407	42130567	JUNC00000001	4	+	GT-AG	0	0	0	D	1	0	0	NDUFA6-AS1	ENSG00000237037	ENST00000439129	22:42129188-42129189
-position = 22:42128881-42128882
-position = 22:42129670-42129671
-22	42128880	42129672	JUNC00000002	3	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
-position = 22:42128944-42128945
-position = 22:42129031-42129032
-22	42128943	42129033	JUNC00000003	4	-	GT-GG	1	0	0	D	1	0	0	CYP2D6	ENSG00000100197	ENST00000360608,ENST00000389970,ENST00000488442	22:42129188-42129189
-position = 22:42129783-42129784
-position = 22:42143453-42143454
-22	42129782	42143455	JUNC00000004	2	+	GC-AG	9	8	9	N	0	0	0	NA	NA	NA	22:42129188-42129189
-position = 22:42130224-42130225
-position = 22:42130565-42130566
-22	42130223	42130567	JUNC00000005	2	+	GT-AG	0	0	0	N	0	0	0	NA	NA	NA	22:42129188-42129189
+22	93668	97252	JUNC00000001	5	+	GT-AG	1	1	1	NDA	1	1	0	EP300	ENSG00000100393	ENST00000263253	22:94626-94627
 ```
 
 For information about the individual RegTools commands, please see [the Commands page](commands/commands.md)