Hy Everybody,
i have a fasta file with a lots of miRNAsequences. The problem is that we have done a concameration experiment before run on 454 machine. So now i have this situation:
>1
AdaptorA__miRNA_AdaptorB
>2
XXXXXX-AdaptorA_ miRNA_AdaptorB_XXXXXX_AdaptorA_miRNA_AdaptorB
etc. ( XXX.. are random nucleotides)
How can i extract sequences between the two adaptors considering that some reads may present the possibilities to have until 4 miRNA ( wiht 4 adaptorA and 4 AdaporB) ???
Can anyone suggest me a script so to not loose any miRNA ??? Thank you very much
Giorgio
i have a fasta file with a lots of miRNAsequences. The problem is that we have done a concameration experiment before run on 454 machine. So now i have this situation:
>1
AdaptorA__miRNA_AdaptorB
>2
XXXXXX-AdaptorA_ miRNA_AdaptorB_XXXXXX_AdaptorA_miRNA_AdaptorB
etc. ( XXX.. are random nucleotides)
How can i extract sequences between the two adaptors considering that some reads may present the possibilities to have until 4 miRNA ( wiht 4 adaptorA and 4 AdaporB) ???
Can anyone suggest me a script so to not loose any miRNA ??? Thank you very much
Giorgio
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