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minor doc fix

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zlskidmore committed Aug 7, 2017
1 parent 27e1b21 commit 1a43d171d83bed96bada2380a58b7d0898d8b928
Showing with 1 addition and 1 deletion.
  1. +1 −1 docs/commands/cis-ase-identify.md
@@ -10,7 +10,7 @@ The `cis-ase identify` command is used to identify allele-specific expression ev
| somatic-variants.vcf | Somatic variant calls in VCF format. The tool looks for allele specific expression at polymorphic loci near the somatic variants|
| polymorphisms.vcf | List of polymorphic loci in the VCF format. RNA expression is checked at these sites to identify evidence of allele speciific expression|
| dna-alignments.bam | Aligned DNA reads in the BAM format that has been indexed for example with `samtools index`. We have tested this command with alignments from BWA.|
| dna-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.|
| rna-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.|
| 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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