-
Notifications
You must be signed in to change notification settings - Fork 0
/
CRI-BIO-646.tree.txt
129 lines (129 loc) · 4.26 KB
/
CRI-BIO-646.tree.txt
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
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
.
|-- Build_RNAseq.CRI-BIO-646.sh
|-- CRI-BIO-646
| |-- CRI-BIO-646.metadata.txt
| |-- CRI-BIO-646.pipeline.yaml
| |-- data
| | |-- 180216_K00242_0355_AHT7NTBBXX-RKeenan-AA-RS10
| | | `-- FastQ
| | | |-- BK-AA-1_S11_L007_R1_001.fastq.gz
| | | |-- BK-AA-2_S12_L007_R1_001.fastq.gz
| | | |-- BK-AA-3_S13_L007_R1_001.fastq.gz
| | | |-- BK-AA-4_S14_L007_R1_001.fastq.gz
| | | |-- BK-AA-5_S15_L007_R1_001.fastq.gz
| | | `-- BK-AA-6_S16_L007_R1_001.fastq.gz
| | `-- 180223_K00242_0357_AHT37VBBXX-RKeenan-AA-RS10
| | `-- FastQ
| | |-- BK-AA-1_S11_L007_R1_001.fastq.gz
| | |-- BK-AA-2_S12_L007_R1_001.fastq.gz
| | |-- BK-AA-3_S13_L007_R1_001.fastq.gz
| | |-- BK-AA-4_S14_L007_R1_001.fastq.gz
| | |-- BK-AA-5_S15_L007_R1_001.fastq.gz
| | `-- BK-AA-6_S16_L007_R1_001.fastq.gz
| `-- references
| `-- v28_92_GRCh38.p12
| |-- GRCh38_rRNA.bed
| |-- GRCh38_rRNA.bed.interval_list
| |-- STAR
| | |-- Genome
| | |-- Log.out
| | |-- SA
| | |-- SAindex
| | |-- chrLength.txt
| | |-- chrName.txt
| | |-- chrNameLength.txt
| | |-- chrStart.txt
| | |-- exonGeTrInfo.tab
| | |-- exonInfo.tab
| | |-- geneInfo.tab
| | |-- genomeParameters.txt
| | |-- run_genome_generate.logs
| | |-- sjdbInfo.txt
| | |-- sjdbList.fromGTF.out.tab
| | |-- sjdbList.out.tab
| | `-- transcriptInfo.tab
| |-- genes.gtf
| |-- genes.gtf.bed12
| |-- genes.refFlat.txt
| |-- genome.chrom.sizes
| |-- genome.dict
| `-- genome.fa
`-- SRC
|-- Python
| |-- build_rnaseq.py
| |-- lib
| | |-- __init__.py
| | |-- __pycache__
| | | |-- __init__.cpython-36.pyc
| | | |-- clusterprofiler.cpython-36.pyc
| | | |-- deseq2.cpython-36.pyc
| | | |-- edger.cpython-36.pyc
| | | |-- fastqc.cpython-36.pyc
| | | |-- limma.cpython-36.pyc
| | | |-- pca.cpython-36.pyc
| | | |-- pheatmap.cpython-36.pyc
| | | |-- picard.cpython-36.pyc
| | | |-- rseqc.cpython-36.pyc
| | | |-- sambamba.cpython-36.pyc
| | | |-- star.cpython-36.pyc
| | | |-- subread.cpython-36.pyc
| | | `-- venn.cpython-36.pyc
| | |-- clusterprofiler.py
| | |-- deseq2.py
| | |-- edger.py
| | |-- fastqc.py
| | |-- limma.py
| | |-- pca.py
| | |-- pheatmap.py
| | |-- picard.py
| | |-- rseqc.py
| | |-- sambamba.py
| | |-- star.py
| | |-- subread.py
| | `-- venn.py
| |-- module
| | |-- __init__.py
| | |-- __pycache__
| | | |-- __init__.cpython-36.pyc
| | | |-- alignread.cpython-36.pyc
| | | |-- alnqc.cpython-36.pyc
| | | |-- callloci.cpython-36.pyc
| | | |-- locistat.cpython-36.pyc
| | | |-- makemasterbds.cpython-36.pyc
| | | |-- mergealn.cpython-36.pyc
| | | |-- postana.cpython-36.pyc
| | | |-- quantification.cpython-36.pyc
| | | |-- quantqc.cpython-36.pyc
| | | `-- readqc.cpython-36.pyc
| | |-- alignread.py
| | |-- alnqc.py
| | |-- callloci.py
| | |-- locistat.py
| | |-- makemasterbds.py
| | |-- mergealn.py
| | |-- postana.py
| | |-- quantification.py
| | |-- quantqc.py
| | `-- readqc.py
| `-- util
| |-- AutoVivification.py
| |-- __init__.py
| |-- __pycache__
| | |-- __init__.cpython-36.pyc
| | |-- ddictfunc.cpython-36.pyc
| | `-- hashlib.cpython-36.pyc
| |-- ddictfunc.py
| `-- hashlib.py
`-- R
|-- module
| |-- DESeq2.R
| |-- PCA.R
| |-- Venn.R
| |-- clusterProfiler.R
| |-- edgeR.R
| |-- limma.R
| `-- pheatmap.R
`-- util
|-- argparse.R
|-- prerequisite.packages.R
`-- pylogger.R