Hi all,
I've got many short sequences like the following:
ADAPTER1 (or 2) + insert + Poly(A) + GGGG(n) + ADAPTER 1 ( or 2)
I'd like to get the insert part for mapping. Also I need to record the adapter type, the length of poly(A) tail and length of GGGG(n) part.
Because it is more than just adpater trimming, I think it is better to write a script to record and trim the adapter, poly(A), GGGG(n) by myself. I can only write some Perl scripts.
But there should be some insertions or deletions in the adapter/polyA/GGG. Is there any Perl function or BioPerl function or some tool/package can search substrings with insertion/deletions/substitution?
Thank you!
I've got many short sequences like the following:
ADAPTER1 (or 2) + insert + Poly(A) + GGGG(n) + ADAPTER 1 ( or 2)
I'd like to get the insert part for mapping. Also I need to record the adapter type, the length of poly(A) tail and length of GGGG(n) part.
Because it is more than just adpater trimming, I think it is better to write a script to record and trim the adapter, poly(A), GGGG(n) by myself. I can only write some Perl scripts.
But there should be some insertions or deletions in the adapter/polyA/GGG. Is there any Perl function or BioPerl function or some tool/package can search substrings with insertion/deletions/substitution?
Thank you!
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