This repository has been archived by the owner on Nov 21, 2019. It is now read-only.
forked from jlanga/ttin_snps
-
Notifications
You must be signed in to change notification settings - Fork 1
/
config.yaml
73 lines (62 loc) · 2.3 KB
/
config.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
rna_pe:
BW-330:
forward: data/fastq_raw/BW-330_1.fastq.gz
reverse: data/fastq_raw/BW-330_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
condition: brain_female
BW-389:
forward: data/fastq_raw/BW-389_1.fastq.gz
reverse: data/fastq_raw/BW-389_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
condition: brain_male
MW-330:
forward: data/fastq_raw/MW-330_1.fastq.gz
reverse: data/fastq_raw/MW-330_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
condition: muscle_female
MW-389:
forward: data/fastq_raw/MW-389_1.fastq.gz
reverse: data/fastq_raw/MW-389_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
condition: muscle_male
MWH-377:
forward: data/fastq_raw/MWH-377_1.fastq.gz
reverse: data/fastq_raw/MWH-377_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
condition: muscle_female
MWT-240:
forward: data/fastq_raw/MWT-240_1.fastq.gz
reverse: data/fastq_raw/MWT-240_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
condition: muscle_male
dna_pe:
western:
forward: data/fastq_raw/C6KB3ANXX_3_10nf_1.fastq.gz
reverse: data/fastq_raw/C6KB3ANXX_3_10nf_2.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
eastern:
forward: data/fastq_raw/C6KB3ANXX_8_14nf_1.fastq.gz
reverse: data/fastq_raw/C6KB3ANXX_8_14nf_1.fastq.gz
adaptor: ./src/Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa
phred: phred33
assembly:
data/assembly/all_normalized.fasta
pep:
data/transdecoder/ttin.pep
software:
kallisto: ./bin/kallisto
trimmomatic: java -jar ./src/Trimmomatic-0.33/trimmomatic-0.33.jar
gzip: pigz
samtools: ./bin/samtools
bcftools: ./bin/bcftools
trimmomatic_params:
SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25 TOPHRED33
kallisto_params:
--bootstrap-samples=100