How To Detect And Remove Loxp Sequence Form Mate Pair Reads

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11.7 years ago

litiancheng.gansu ▴ 10

I have some mate pair data to analysis, could any one give me some suggestion about how to detect and remove loxp sequence in the mate pair reads.

I have found the R script: DeLoxer which seems could do my job, but I tested it and it eat all of my server memory, what more, it's performance is so bad that it's too slow to deal all of my data. Do some other tools which can do this job?

LoxP is a 42nt sequence, it incorporated at the junction site between the outer end of a long sequence. Here is about Cre-Lox description: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273786/ LoxP adapter oligos

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ADD COMMENT • link 11.7 years ago by litiancheng.gansu ▴ 10

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can you remind us what is a loxp sequence please....

ADD REPLY • link 11.7 years ago by Pierre Lindenbaum 164k

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If the sequence is at either end of the read you could remove it with any adapter removal program.

ADD REPLY • link 11.7 years ago by fo3c ▴ 450

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