|
13
|
1 ==============================
|
|
|
2 README for TEiso
|
|
|
3 ==============================
|
|
|
4 ------------------------------------------------------------
|
|
|
5 ======================= dependencies =======================
|
|
|
6 ------------------------------------------------------------
|
|
|
7
|
|
|
8 Bowtie, Tophat, Cufflinks, Cuffcompare, Bedtools_closest.
|
|
|
9
|
|
|
10 ------------------------------------------------------------
|
|
|
11 ===================== INSTALLATION =========================
|
|
|
12 ------------------------------------------------------------
|
|
|
13
|
|
|
14 $tar -xzf TEiso-1.2.tar.gz
|
|
|
15 $cd TEiso-1.2/
|
|
|
16 $python setup_TEiso.py install
|
|
|
17 $export PYTHONPATH=$PWD
|
|
|
18 $export PATH=$PATH:$PWD/bin
|
|
|
19
|
|
|
20
|
|
|
21
|
|
|
22 ------------------------------------------------------------
|
|
|
23 ======================== description =======================
|
|
|
24 ------------------------------------------------------------
|
|
|
25
|
|
|
26 TEiso is a python script that allows to find distance between the element transposable and TSS of isoforms :
|
|
|
27
|
|
|
28
|
|
|
29 ------------------------------------------------------------
|
|
|
30 ===================== command examples =====================
|
|
|
31 ------------------------------------------------------------
|
|
|
32 if reads are single:
|
|
|
33 LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e single -s <single_read> -t <TE.gff> -a cufflinks
|
|
|
34 if reads are paired:
|
|
|
35 LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e paired -l <reads_left> -r <reads_right> -t <TE.gff> -a cufflinks
|
|
|
36
|
|
|
37 ------------------------------------------------------------
|
|
|
38 ========================== options =========================
|
|
|
39 ------------------------------------------------------------
|
|
|
40
|
|
|
41 --version show program's version number and exit
|
|
|
42 -h, --help show this help message and exit
|
|
|
43
|
|
|
44 -f INPUT_REFERENCE, --input_reference=INPUT_REFERENCE
|
|
|
45 file with ref sequences
|
|
|
46
|
|
|
47 -g INPUT_TRANSCRIPTS, --input_transcripts=INPUT_TRANSCRIPTS
|
|
|
48 GTF/GFF with known transcripts
|
|
|
49
|
|
|
50 -e SINGLE_PAIRED, --single_paired=SINGLE_PAIRED
|
|
|
51 type of input reads, single or paired end
|
|
|
52
|
|
|
53 -s SINGLE_READ, --single_read=SINGLE_READ
|
|
|
54 a single input read
|
|
|
55
|
|
|
56 -l LEFT_READ, --left_read=LEFT_READ
|
|
|
57 left reads
|
|
|
58
|
|
|
59 -r RIGTH_READ, --rigth_read=RIGTH_READ
|
|
|
60 right reads
|
|
|
61
|
|
|
62 -t INPUT_TRANSPOSABLE_ELEMENT, --input_transposable_element=INPUT_TRANSPOSABLE_ELEMENT
|
|
|
63 GFF with known transposable_element
|
|
|
64
|
|
|
65 -a ASSEMBLY_TOOL, --assembly_tool=ASSEMBLY_TOOL
|
|
|
66 type of RNA-Seq assembly tool
|
|
|
67
|
|
|
68 -
|
