Update cis-splice-effects-identify.md

Author: yang-yangfeng

docs/commands/cis-splice-effects-identify.md

@@ -1,7 +1,7 @@
 [csei]: ../images/csei_examples.png
 
 ###Synopsis
-The `cis-splice-effects identify` command is used to identify splicing misregulation events. This command takes in a list of variants in the VCF format and RNAseq alignments produced with a splice-aware aligner in the BAM format. The tool then proceeds to identify non-canonical splicing junctions near the variant sites.
+The `cis-splice-effects identify` command is used to identify splicing misregulation events. This command takes in a list of variants in the VCF format and RNAseq alignments produced with a splice-aware aligner in the BAM/CRAM format. The tool then proceeds to identify non-canonical splicing junctions near the variant sites.
 
 ###Usage
 `regtools cis-splice-effects identify [options] variants.vcf alignments.bam ref.fa annotations.gtf`
@@ -10,7 +10,7 @@ The `cis-splice-effects identify` command is used to identify splicing misregula
 | Input                  | Description |
 | ------                 | ----------- |
 | variants.vcf | Variant call in VCF format from which to look for cis-splice-effects.|
-| alignments.bam | Aligned RNAseq BAM produced with a splice aware aligner, that has been indexed for example with `samtools index`. We have tested this command with alignments from TopHat.|
+| 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.|
 | 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/).|