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----------------------------
Tag Find Application
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This script searches for a specific 12 nucleotide long tag sequence
used during the preparation of the cDNA library for RNA-seq experiments, 
annotates the start and end position of the tag within the read and the type of
tag found, together with the read length, in a text file and then eliminates
the tag from the read sequence. It recognizes tags with at most one nucletide error
(mismatch/insertion/deletion) within their sequence and assign a specific label to 
each tags found. Tag sequences were designed by the Institute of Biomedical Technologies,
National Research Council of Bari, Italy. Tag Find was designed and developed by 
Claudia Calabrese, University of Bologna, Italy.

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Tag Find Usage
----------------------------

Tag Find is written in Python and was tested with Python 2.6 and can be downloaded and run
as a standalone package by the user. Tag Find requires a python interpreter (version 2.5
 or higher) and the installation of the Biopython module. Tag Find is platform independent
tool. The python interpreter and the Biopython module can be downloaded from 
http://python.org/ and http://biopython.org/wiki/Download, respectively. 
Tag Find uses as input a fastq file and an integer value corresponding to the length 
threshold fixed by the user in order to filter out reads shorter than this value. 
Tag Find can be launched with this command line:

          python Tag_Find.py 454seq_simulation.fastq 40

Where 40 is the length threshold used in this example. To eliminate any filtering, a value
of 0 must be used.

For more information please refer to Calabrese C, Mangiulli M, Manzari C, Paluscio AM, 
Caratozzolo MF, Marzano F,Kurelac I, D Erchia AM, D Elia D, Licciulli F, Liuni S, Picardi E,
Attimonelli M, Gasparre G, Porcelli AM, Pesole G, Sbisà E, Tullo A. A platform independent 
RNA-Seq protocol for the detection of transcriptome complexity. BMC Genomics. 2013 Dec 5;14(1):855.
[Epub ahead of print] PubMed PMID: 24308330.

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Contact
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claudia.calabrese23@gmail.com
Source: README.txt, updated 2013-12-10