adrec

Note:All the below doc is updated and only are here for historical reason. Ignore this section. Go to the main README for the current working tool

###Adapter recognition and removal from reads (MacOSX and Linux)

Remove 3' adapters from Illumina reads TGAGGTAGTAGTTTGTAC*ATCTCGTATGCCGTCTTCT* => TGAGGTAGTAGTTTGTAC

==Cite==

SeqBuster is a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Pantano L, Estivill X, Martí E. Nucleic Acids Res. 2010 Mar;38(5):e34. Epub 2009 Dec 11.

==USAGE==

java -jar seqbuster/adrec/adrec.jar -i seqbuster/adrec/test/test.fastq -a ATCTCGTATGCCGTCTTCTGCTTG -m 1 -l 8 -c 0.3 -s 15 -e 40 -o seqbuster/adrec/test/test

Vide tutorial

==MANUAL==

• Parameter i fasta/fastq file
• Parameter a adapter
• Parameter m number of mismatches allowed at the adapter
• Parameter l length of adapter recognized
• Parameter c complexity ratio
• Parameter s minimum size sequence accepted (only dev version)
• Parameter e maximum size sequence accepted (only dev version)

==OUTPUT==

Format is not normal fasta
Go to adapter recognition...
Mismatches: 1
Length to be recognized: 8
Complexity threshold: 0.3
Adapter: TGGAATTCTCGGGTGCCAAGG
Writing file to upload to the SeqBuster Server...

Writing sequences: 2515 

Number of sequences added: 1970

A complete report is in: test/test.fastq.info
Process finished at: Wed May 18 16:35:15 CEST 2011

==OUTPUTS== You have examples inside the test folder:

• namefile.ad= sequences were adapter has been detected
• namefile.info=information about the process
• namefile.longer=sequences longer than 40 nt
• namefile.noad=sequence without adapter
• namefile.complex=high repetitive sequences