Mercurial > repos > urgi-team > teiso
comparison TEisotools-1.1.a/TEiso/doc/README_TEiso.txt @ 13:feef9a0db09d draft
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| author | urgi-team |
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| date | Wed, 20 Jul 2016 09:04:42 -0400 |
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| 12:22b0494ec883 | 13:feef9a0db09d |
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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 - |