Mercurial > repos > urgi-team > teiso
comparison TEisotools-1.1.a/TEiso/doc/README_TEiso.txt @ 16:836ce3d9d47a draft default tip
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author | urgi-team |
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date | Thu, 21 Jul 2016 07:42:47 -0400 |
parents | 255c852351c5 |
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15:255c852351c5 | 16:836ce3d9d47a |
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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 - |