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1 ==============================
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2 README for TEiso
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3 ==============================
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4 ------------------------------------------------------------
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5 ======================= dependencies =======================
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6 ------------------------------------------------------------
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7
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8 Bowtie, Tophat, Cufflinks, Cuffcompare, Bedtools_closest.
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9
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10 ------------------------------------------------------------
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11 ===================== INSTALLATION =========================
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12 ------------------------------------------------------------
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13
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14 $tar -xzf TEiso-1.2.tar.gz
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15 $cd TEiso-1.2/
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16 $python setup_TEiso.py install
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17 $export PYTHONPATH=$PWD
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18 $export PATH=$PATH:$PWD/bin
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19
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20
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21
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22 ------------------------------------------------------------
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23 ======================== description =======================
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24 ------------------------------------------------------------
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25
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26 TEiso is a python script that allows to find distance between the element transposable and TSS of isoforms :
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27
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28
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29 ------------------------------------------------------------
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30 ===================== command examples =====================
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31 ------------------------------------------------------------
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32 if reads are single:
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33 LaunchTEiso.py -f <genome.fa> -g <transcripts.gtf> -e single -s <single_read> -t <TE.gff> -a cufflinks
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34 if reads are paired:
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35 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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36
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37 ------------------------------------------------------------
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38 ========================== options =========================
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39 ------------------------------------------------------------
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40
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41 --version show program's version number and exit
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42 -h, --help show this help message and exit
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43
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44 -f INPUT_REFERENCE, --input_reference=INPUT_REFERENCE
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45 file with ref sequences
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46
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47 -g INPUT_TRANSCRIPTS, --input_transcripts=INPUT_TRANSCRIPTS
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48 GTF/GFF with known transcripts
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49
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50 -e SINGLE_PAIRED, --single_paired=SINGLE_PAIRED
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51 type of input reads, single or paired end
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52
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53 -s SINGLE_READ, --single_read=SINGLE_READ
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54 a single input read
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55
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56 -l LEFT_READ, --left_read=LEFT_READ
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57 left reads
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58
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59 -r RIGTH_READ, --rigth_read=RIGTH_READ
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60 right reads
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61
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62 -t INPUT_TRANSPOSABLE_ELEMENT, --input_transposable_element=INPUT_TRANSPOSABLE_ELEMENT
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63 GFF with known transposable_element
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64
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65 -a ASSEMBLY_TOOL, --assembly_tool=ASSEMBLY_TOOL
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66 type of RNA-Seq assembly tool
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67
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68 -
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