comparison TEisotools-1.1.a/TEiso/doc/README_TEiso.txt @ 16:836ce3d9d47a draft default tip

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date Thu, 21 Jul 2016 07:42:47 -0400
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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 -