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

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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
author iuc
date Sat, 27 Jan 2024 12:34:39 +0000
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-1:000000000000 0:462e62be07e1
1 VARVAMP log
2
3 MODE = qpcr
4
5
6 ARG SETTINGS
7
8 THRESHOLD = 0.7
9 PRIMER_ALLOWED_N_AMB = 1
10 PROBE_ALLOWED_N_AMB = 1
11 TEST_DELTAG_N_AMPLICONS = 180
12 DELTAG_CUTOFF = -15
13
14 CONFIG SETTINGS
15
16 PRIMER_TMP = (56, 63, 60)
17 PRIMER_GC_RANGE = (35, 65, 50)
18 PRIMER_SIZES = (18, 24, 21)
19 PRIMER_HAIRPIN = 47
20 PRIMER_MAX_POLYX = 4
21 PRIMER_MAX_DINUC_REPEATS = 4
22 PRIMER_GC_END = (1, 3)
23 PRIMER_MAX_DIMER_TMP = 47
24 PRIMER_MIN_3_WITHOUT_AMB = 3
25 PCR_MV_CONC = 100
26 PCR_DV_CONC = 2
27 PCR_DNTP_CONC = 0.8
28 PCR_DNA_CONC = 15
29 PRIMER_TM_PENALTY = 2
30 PRIMER_GC_PENALTY = 0.2
31 PRIMER_SIZE_PENALTY = 0.5
32 PRIMER_MAX_BASE_PENALTY = 10
33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
34 PRIMER_PERMUTATION_PENALTY = 0.1
35 QPROBE_TMP = (64, 70, 67)
36 QPROBE_SIZES = (20, 30, 25)
37 QPROBE_GC_RANGE = (40, 80, 60)
38 QPROBE_GC_END = (0, 4)
39 QPRIMER_DIFF = 2
40 QPROBE_TEMP_DIFF = (5, 10)
41 QPROBE_DISTANCE = (4, 15)
42 QAMPLICON_LENGTH = (70, 200)
43 QAMPLICON_GC = (40, 60)
44 QAMPLICON_DEL_CUTOFF = 4
45