Mercurial > repos > urgi-team > teiso

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README for TEiso
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======================= dependencies =======================
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Bowtie, Tophat, Cufflinks, Cuffcompare, Bedtools_closest.

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===================== INSTALLATION =========================
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$tar -xzf TEiso-1.2.tar.gz
$cd TEiso-1.2/
$python setup_TEiso.py install
$export PYTHONPATH=$PWD
$export PATH=$PATH:$PWD/bin


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======================== description =======================
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TEiso is a python script that allows to find distance between the element transposable and TSS of isoforms :


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===================== command examples =====================
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if reads are single:
     LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e single -s <single_read> -t <TE.gff> -a cufflinks
if reads are paired:
     LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e paired -l <reads_left> -r <reads_right> -t <TE.gff> -a cufflinks

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========================== options =========================
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  --version             show program's version number and exit
  -h, --help            show this help message and exit

  -f INPUT_REFERENCE,   --input_reference=INPUT_REFERENCE
                        file with ref sequences

  -g INPUT_TRANSCRIPTS, --input_transcripts=INPUT_TRANSCRIPTS
                        GTF/GFF with known transcripts

  -e SINGLE_PAIRED, --single_paired=SINGLE_PAIRED
                        type of input reads, single or paired end

  -s SINGLE_READ, --single_read=SINGLE_READ
                        a single input read

  -l LEFT_READ, --left_read=LEFT_READ
                        left reads

  -r RIGTH_READ, --rigth_read=RIGTH_READ
                        right reads

  -t INPUT_TRANSPOSABLE_ELEMENT, --input_transposable_element=INPUT_TRANSPOSABLE_ELEMENT
                        GFF with known transposable_element

  -a ASSEMBLY_TOOL, --assembly_tool=ASSEMBLY_TOOL
                        type of RNA-Seq assembly tool

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author	urgi-team
date	Thu, 21 Jul 2016 07:36:44 -0400
parents	feef9a0db09d
children