update README

Snakemake/1000RNASeq_chicken/ASE/README.md

@@ -18,9 +18,9 @@ This pipeline will perform variant filtering, reads alignment on masked genome a
 
 The user must use the [config_calling.yaml](config_calling.yaml.example) file to provide all necessary inputs for the pipeline:
 
-- A masked reference fasta file (fasta_ref option), indexed with samtools faidx and GATK4 CreateSequenceDictionary
+- A masked reference fasta file (fasta_ref option), indexed with samtools faidx and GATK4 CreateSequenceDictionary. We recommend to mask genome with variant filtered bi-allelic and on GATK metrics FS < 30, QD > 2 and AF < 1. In our used case we mask genome on variant construct at the population level, and then we launch this pipeline at the tissue level.
 
-- A genome reference GTF file (gtf_ref option)
+- An genome annotation reference GTF file (gtf_ref option)
 
 - A set of variant to include in the ASE analysis
 
@@ -47,6 +47,8 @@ The user must use the [config_calling.yaml](config_calling.yaml.example) file to
 
 First step is to filter and trim raw reads before alignment. This step will convert phred 64 scale fastq files into phred 33 scale fastq files and then trim reads with [trim_galore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). It will trim adapter and filtered out trimmed reads that are smaller than the third of the read length.
 
+By default the trimming quality threshold is set to 15.
+
 You will find in Result/Summary directory, a Log_TrimGalore_summary.tsv that detail the trim_galor statistics.
 
 
@@ -77,7 +79,7 @@ Finally reads that contain Ns in their cigar string will be splittd, and alignme
 
 Variants will be filtered before submitting to ASE.
 
-Only SNP with FS < or equal to 30.0 and QD < or equal to 2.0 will be used in ASE.
+Only bi-allelic SNP with FS < or equal to 30.0 and QD < or equal to 2.0 will be used in ASE.
 
 Filtering on SNP type is an option, see SNP_filter in the configuration file. By default it is set to False as the calling pipeline generate output VCF file filtered on SNP type.