[Bioperl-l] Scripting help to identify adaptors count in reads

Giorgio C casaburi at ceinge.unina.it
Thu Nov 10 07:29:55 EST 2011


Hi everybody,

i have some reads (454) where there are adaptors (NNNN...), one,two or three
adaptors for each reads depending on the reads. Is there any way to
establish how many reads have 1 adaptors, how many 2 and how many 3 adaptors
over the total ???

>271-88
GCCTTGCCAGCCGCTCAGATTGATNNNNNNNNNNNNNNNATCAGGTGCCTACG
>272-88
GCCTTGCCAGCCGCTCAGATTGATNNNNNNNNNNNNNNNATCANNNNNNNNNNNNNNNCTGATGGCGCGAGGGAGGCGCCTTGCCAGCCCGCTCAGATTGATNNNNNNNNNNNNNNNCTGATGGCGCGAGGGAGGC
>273-88
GCCTCCCTCGCGCATCAGATCGTAGGCACCATCAATCTGAGCGGGCTGGCAAGGCGCCTCCCTCGCGCCA
>274-88
GCCTTGCCAGCCGCTCAGATTGATNNNNNNNNNNNNNNNCTGATGGCGCGAGGGAGGCGCCTCCCTCGCGCCATCAGATCGTNNNNNNNNNNNNNNNNNNTCGTAGGCACCATCAATCTGAGCGGGCTGGCAAGGCGCCTCCCTCGCGCCATCAGATCGTAGGCACCATCAA

The problem is that some adpators occur in the middle of the sequences
because they coming out from a concameration experimental design (they are
miRNAs between NNNNNN...). So i want to know a script or tool that may say
how many reads have 1 adapt, how many 2, (max are 4) in respect to the total
number of reads. Do you know any tool/script that may help ? Tnx 
Can anyone suggests me a script to fix this ???

Thank you very much 
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