diff test-data/test3.log @ 0:462e62be07e1 draft

planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
author iuc
date Sat, 27 Jan 2024 12:34:39 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3.log	Sat Jan 27 12:34:39 2024 +0000
@@ -0,0 +1,45 @@
+VARVAMP log 
+
+MODE = qpcr
+
+
+ARG SETTINGS
+
+THRESHOLD = 0.7
+PRIMER_ALLOWED_N_AMB = 1
+PROBE_ALLOWED_N_AMB = 1
+TEST_DELTAG_N_AMPLICONS = 180
+DELTAG_CUTOFF = -15
+
+CONFIG SETTINGS
+
+PRIMER_TMP = (56, 63, 60)
+PRIMER_GC_RANGE = (35, 65, 50)
+PRIMER_SIZES = (18, 24, 21)
+PRIMER_HAIRPIN = 47
+PRIMER_MAX_POLYX = 4
+PRIMER_MAX_DINUC_REPEATS = 4
+PRIMER_GC_END = (1, 3)
+PRIMER_MAX_DIMER_TMP = 47
+PRIMER_MIN_3_WITHOUT_AMB = 3
+PCR_MV_CONC = 100
+PCR_DV_CONC = 2
+PCR_DNTP_CONC = 0.8
+PCR_DNA_CONC = 15
+PRIMER_TM_PENALTY = 2
+PRIMER_GC_PENALTY = 0.2
+PRIMER_SIZE_PENALTY = 0.5
+PRIMER_MAX_BASE_PENALTY = 10
+PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
+PRIMER_PERMUTATION_PENALTY = 0.1
+QPROBE_TMP = (64, 70, 67)
+QPROBE_SIZES = (20, 30, 25)
+QPROBE_GC_RANGE = (40, 80, 60)
+QPROBE_GC_END = (0, 4)
+QPRIMER_DIFF = 2
+QPROBE_TEMP_DIFF = (5, 10)
+QPROBE_DISTANCE = (4, 15)
+QAMPLICON_LENGTH = (70, 200)
+QAMPLICON_GC = (40, 60)
+QAMPLICON_DEL_CUTOFF = 4
+