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

Uploaded

--- a/TEisotools-1.1.a/TEiso/doc/README_TEiso.txt	Thu Jul 21 07:36:44 2016 -0400
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-==============================
-README for TEiso
-==============================
-------------------------------------------------------------
-======================= dependencies =======================
-------------------------------------------------------------
-
-Bowtie, Tophat, Cufflinks, Cuffcompare, Bedtools_closest.
-
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-===================== INSTALLATION =========================
-------------------------------------------------------------
-
-$tar -xzf TEiso-1.2.tar.gz
-$cd TEiso-1.2/
-$python setup_TEiso.py install
-$export PYTHONPATH=$PWD
-$export PATH=$PATH:$PWD/bin
-
-
-
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-======================== description =======================
-------------------------------------------------------------
-
-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
-
-------------------------------------------------------------
-========================== options =========================
-------------------------------------------------------------
-
-  --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
-
--