From fae437864cf4ec28c18f18ea886060063d14a9cf Mon Sep 17 00:00:00 2001 From: John Beaulaurier Date: Mon, 26 Feb 2018 13:39:06 -0800 Subject: [PATCH] Updated usage instructions --- smalr/SmalrConfig.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/smalr/SmalrConfig.py b/smalr/SmalrConfig.py index 51f7307..dba6fb0 100644 --- a/smalr/SmalrConfig.py +++ b/smalr/SmalrConfig.py @@ -20,10 +20,14 @@ def __parseArgs( self ): The inputs_file has the following format: native_cmph5 : /path/to/native/aligned_reads.cmp.h5 - fastq : /path/to/native/CCS_reads.fastq (optional) + fastq : /path/to/native/CCS_reads.fastq (DEPRECATED; specify NONE) wga_cmph5 : /path/to/WGA/aligned_reads.cmp.h5 ref : /path/to/sample/reference.fasta + With the updated support for aligned BAM files (in addition to *.cmp.h5 files), + please supply the path to the aligned BAM file using the 'native_cmph5' and + 'wga_cmph5' lines in the input file. + SMsn: Single-molecule, single nucleotide analysis Each motif site on each sequencing molecule is assessed for methylation