I've got some MiSeq data from Nextera XT prepped libraries. I figure that it will be necessary to trim adapters and/or transposase sequences from the data and I'm hoping someone can assist me. I'd like to use Scythe for trimming.
Scythe requires an adapters/contaminants file (FASTA format) as input, and I'm confused as to how to construct this file. Illumina provides the following information on the sequences:
Nextera® transposase sequences
5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
(a) Read 1 -->
5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
(d) Read 2 -->
Nextera® Index Kit - PCR primers
5’ AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC
(c) i5 Index read -->
5’ CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG
<-- i7 Index read (b)
Could I simply use the following adapter FASTA file content? (I've combined the adapter and transposase sequences into single string using the overlapping region.) What do I replace the [i5] and [i7] barcode tags with?
>FWD_Adapter
AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>REV_Adapter
CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
Thanks for any help you can provide!
Scythe requires an adapters/contaminants file (FASTA format) as input, and I'm confused as to how to construct this file. Illumina provides the following information on the sequences:
Nextera® transposase sequences
5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
(a) Read 1 -->
5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
(d) Read 2 -->
Nextera® Index Kit - PCR primers
5’ AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC
(c) i5 Index read -->
5’ CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG
<-- i7 Index read (b)
Could I simply use the following adapter FASTA file content? (I've combined the adapter and transposase sequences into single string using the overlapping region.) What do I replace the [i5] and [i7] barcode tags with?
>FWD_Adapter
AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>REV_Adapter
CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
Thanks for any help you can provide!
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