From ad85e0cc42a27495833b5fb3ac8279382353ff77 Mon Sep 17 00:00:00 2001 From: Runsheng Date: Wed, 26 Oct 2022 16:38:47 +0800 Subject: [PATCH] typo fix --- readme.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/readme.md b/readme.md index 174a483..da97d77 100644 --- a/readme.md +++ b/readme.md @@ -58,16 +58,18 @@ optional arguments: ``` Use _C. nigoni_ and _C.briggsae_ genomes as example. The two fasta files can be downloaded separately -from [cb4.fa](https://github.com/Runsheng/cbgenome/releases/download/cb5pre_cn3pre/cb5.fa.gz) and +from [cb5.fa](https://github.com/Runsheng/cbgenome/releases/download/cb5pre_cn3pre/cb5.fa.gz) and [cn3_new.fa](https://github.com/Runsheng/cbgenome/releases/download/cb5pre_cn3pre/cn3_new.fa.gz). The _C. nigoni_ genome is cn3_new.fa and _C. briggsae_ genome is cb5.fa. To design _C. briggsae_ unique primer, which would not amplify any region in _C. nigoni_, and amplify only one region in _C. briggsae_. The targeted region for C. briggsae is ChrX:12881200-15106660 (-pos), one primer is designed for every 4kb interval (--interval). -``` +```bash primerdesign.py -g1 cb5.fa -g2 cn3_new.fa -pos "ChrX:12881200-15106660" --interval 4000 +``` +``` # check the result in file "primers_ChrX:12881200-15106660.txt" head primers_ChrX\:12881200-15106660.txt #ChrX:12881200-12881700 GATCCAAAACATGAGTGGCC CGAGATCATTGGCTCAAAGT 287 @@ -104,6 +106,10 @@ optional arguments: ```bash ispcr.py -f gcactttcatgtccctcaac -r cactctattctcaccccacc -g cb5.fa -o ispcr.fa +``` + +``` +# check the PCR product in ispcr.fa head ispcr.fa #>ChrI:230699-231076_RC #GCACTTTCATGTCCCTCAACCAGTCGTTTTTCCTTACCTCTCCCCTTCCTTTTTTCCCCCTCCCAGATGACGTCACCCATCTGTCC @@ -116,6 +122,6 @@ head ispcr.fa ## Roadmap for other functions: 1. To use user-provided primer parameters.Primer design parameter now is fine-tuned for general purpose PCR, which can be found in "general_settings.py".This file may need be modified to generate primers for specific purpose PCR like real-time qPCR. 2. To update the RFLP method for primer design to differ sequences with almost identical sequence. -3. To update the primer design using VCF file. +3. To update the primer design using VCF file for closely related haplotypes. \ No newline at end of file