Differences

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--- strviper [2017/05/03 14:33] – mikael
+++ strviper [2018/03/20 09:48] (current) – mikael
@@ Line 9: / Line 9: @@
 If you are interested in knowing more about STRViper, please contact Minh Duc Cao (minhduc.cao@gmail.com). If you find STRViper useful for your research, please cite it in your publications.
-Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S and Bodén M (2014) Inferring Short Tandem Repeat Variation from Paired-End Short Reads, Nucleic Acids Research. Feb;42(3):e16. DOI: 10.1093/nar/gkt1313.
+Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S and Bodén M (2014) Inferring Short Tandem Repeat Variation from Paired-End Short Reads, //Nucleic Acids Research//. Feb;42(3):e16. DOI: [[http://dx.doi.org/10.1093/nar/gkt1313|10.1093/nar/gkt1313]].
-=== Installation ===
+=== Installation (original version) ===
-. Download the strviper package.
+. Download the strviper package: http://bioinf.scmb.uq.edu.au:8080/STRViper/strviper.tar.gz
 . Unzip the package to $PATH_TO_STRV (i.e., tar zxvf strviper.tar.gz)
 . Add $PATH_TO_STRV/scripts to you $PATH
-=== Making Variations Calls ===
+=== Installation (JAPSA version) ===
+. Download JAPSA from https://github.com/mdcao/japsa
+. Follow instructions there
+=== Call variation (original version) ===
 Preprocessing:
@@ Line 50: / Line 55: @@
 $ jsat.str strv2vcf --input lib.strv --output lib.vcf --reference TAIR10.fas
+=== Call variation (JAPSA version) ===
+As above but note the equivalent programs are in:
+  jsa.trv.parseTRF
+  jsa.trv.sam2fragment
+  jsa.trv.sortFragment
+  jsa.trv.fragment2var