From cfbcca3b9ed8ea334e8d74efe401b61540d3e878 Mon Sep 17 00:00:00 2001 From: Haifeng Chen Date: Sun, 22 Nov 2015 15:42:05 -0800 Subject: [PATCH] Update FAQ.md --- FAQ.md | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/FAQ.md b/FAQ.md index 756a469..9046267 100644 --- a/FAQ.md +++ b/FAQ.md @@ -1,11 +1,18 @@ ## Frequently Asked Questions ## 1. When does WALT get much lower mapping rate (mapping effiency) compared to other bisulfite mappers? - By default, WALT ignores reads shorter than 39. If you get lower mapping rate, please go to mapstats file and check the percentage of reads that are shorter than 39. If a large portion of reads are shorter than 39, I suggest you use WALT seed pattern 7. - (1) Open walt/src/walt/Makefile, modify “-D SEEDPATTERN3" to " -D SEEDPATTERN7" - (2) rebuild the program using make all, make install - (3) rebuild your index using the new makedb command - (4) mapping reads using the new walt command + + By default, WALT ignores reads shorter than 39. If you get lower mapping rate, please go to mapstats file and check the percentage of reads that are shorter than 39. If a large portion of reads are shorter than 39, I suggest you use WALT seed pattern 7. + + (1) Open walt/src/walt/Makefile, modify “-D SEEDPATTERN3" to " -D SEEDPATTERN7" + + (2) rebuild the program using make all, make install + + (3) rebuild your index using the new makedb command + + (4) mapping reads using the new walt command + +