diff TEisotools-1.1.a/TEiso/doc/README_TEiso.txt @ 13:feef9a0db09d draft

Uploaded

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+==============================
+README for TEiso
+==============================
+------------------------------------------------------------
+======================= dependencies =======================
+------------------------------------------------------------
+
+Bowtie, Tophat, Cufflinks, Cuffcompare, Bedtools_closest.
+
+------------------------------------------------------------
+===================== 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
+
+
+
+------------------------------------------------------------
+======================== description =======================
+------------------------------------------------------------
+
+TEiso is a python script that allows to find distance between the element transposable and TSS of isoforms :
+
+
+------------------------------------------------------------
+===================== command examples =====================
+------------------------------------------------------------
+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
+
+-