From bdb36206c93e5916651f0cf33d6f80796b5f0e17 Mon Sep 17 00:00:00 2001 From: Yi Li Date: Thu, 9 Jan 2014 22:52:30 -0800 Subject: [PATCH] Update README.md update to 1.1.1 --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index cf403ca..f51d06a 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -README for PyLOH 1.1 -==================== +README for PyLOH 1.1.1 +====================== INTRODUCTION @@ -95,8 +95,9 @@ cancer sequencing data, execute: $ PyLOH.py preprocess REFERENCE_GENOME.fasta NORMAL.bam TUMOUR.bam BASENAME --segments_bed SEGMENTS.bed --min_depth 20 --min_base_qual 10 --min_map_qual 10 --process_num 10 ``` -**REFERENCE_GENOME.fasta** The path to the fasta file that the paired BAM files aligned to. Note that the index file should be generated -for the reference genome. This can be done by running samtools as follows: +**REFERENCE_GENOME.fasta** The path to the fasta file that the paired BAM files aligned to. Currently, only the +[UCSC](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) and [ENSEMBL](http://uswest.ensembl.org/info/website/upload/bed.html) +chromosome format are supported. Note that the index file should be generated for the reference genome. This can be done by running samtools as follows: `$ samtools faidx REFERENCE_GENOME.fasta`