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Old 07-12-2018, 09:24 PM   #301
kokyriakidis
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Default Different Libraries

Quote:
Originally Posted by GenoMax View Post
Have you looked at the in-line help for "splitnextera.sh"? The adapters for Mate Pair libraries are in the "adapters.fa" file so you should be able to trim them as usual (Nextera_LMP_Read1_External_Adapter, Nextera_LMP_Read2_External_Adapter)
In SplitNextera guide it states that it it different from LMP. Nextera mate pair is not the same as Mate pair library v2 and also, Mate pair library v2 does not have these LMP adapters you mentioned!

From JGI site:
"SplitNextera splits Nextera LMP libraries into subsets based on linker orientation. It is designed strictly for Nextera LMP (long-mate-pair) reads, not for normal libraries using a Nextera kit. Nextera LMP libraries must be split prior to further processing; they are not usable raw. Adapter-trimming should still be done on Nextera LMP libraries prior to splitting."

Mate SamplePrep V2 Documentation:
https://support.illumina.com/content...15008135_A.pdf
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Old 07-13-2018, 09:36 PM   #302
jamie225
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hi. i am new here how are you all.
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Old 07-18-2018, 09:46 PM   #303
jsena33
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Hi All,

Is it possible to match degenerate sequences like below, trim the sequences and place the degenerate sequences in the fastq header? I am attempting to trim an adapter with the following structure Adapter(21nt)-UMI(16nts)-Adapter(24nt) and place it in the fastq header.

Matching degenerate sequences such as primers:
bbduk.sh in=reads.fq out=matching.fq literal=ACGTTNNNNNGTC copyundefined k=13 mm=f

Thank you for your help!
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Old 07-19-2018, 03:57 AM   #304
GenoMax
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@jsena33: You should take a look at UMI tools for this type of application.
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Old 07-19-2018, 06:34 AM   #305
jsena33
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Hi GenoMax,

Thanks for the suggestion! I have used UMI tools which works ok but I am working with long reads with a higher error rate (indel bias) than Illumina reads. Therefore, it is likely that the adapter and UMI will contain indels so the adapter structure may actually look like this, Adapter(19-21nt)-UMI(14-16nts)-Adapter(22-24nt).

Thanks again for your advice!
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