I am working with a Miseq dataset on multiplex bisulfite amplicon sequencing. I have the sequences of the 30 amplicons. How can I make a fasta reference out of them to be used for Bismark alignment?
I have made a fasta file listing the amplicons as the following, but it didn't work with Bismark. I got 0% CpG methylation and 99% CHH methylation. Is there anything wrong with my amplicon reference? Thank you!
>Myh6_1
AATAACTGAGGTAAGGGCCTGGGTAGGGGAGGTGGTGTGAGACGCTCCTGTCTCTCCTCTATCTGCCCATCGGCCCTTTGGGGAGGAGGAATGTGCCCAAGGACTAAAAAAAGGCCATGGAGCCAGAGGGGCGAGGGCAACAGACCTTTCATGGGCAAACCTTGGGGCCCTGCTGTCCTCCTGTCACCTCCAGAGCCAAGGGATCAAAGGAGGAGGAGCCAGGACAGGAGGGAAGTGGGAGGGAGGGTCCCAGCAGAGGACTCCAAATTTAGGCAGCAGGCATATGGGATGGGATATAAAGGGGCTGGAGCACTGAGAGCTGTCAGACAGAGATTTCTCCAACCCAGGTAAGAGGGAGTTTCGGGTGGGGGCTCTTCACCCACACCAGACCTCTCCCCACCTAGAAGGAAACTGCCTTTCCTGGAAGT
>Myh6_2
CCTCCCATCAGGAGTGGAGGGTTGCAGAGGGAGGGTAAAAACCTACATGTCCAAACATCATGGTGCACGATATATGGATCAGTATGTGTAGAGGCAAGAAAGGAAATCTGCAGGCTTAACTGGGTTAATGTGTAAAGTCTGTGTGCATGTGTGTGTGTCTGACTGAAAACGGGCATGGCTGTGCAGCTGTTCAGTTCTGTGCGTGAGGTTACCAGACTGCAGGTTTGTGTGTAAATTGCCCAAGGCAAAGTGGGTGAATCCCTTCCATGGTTTAAAGAGATTGGATGATGGCCTGCATCTCAGGGACCATGGAAAATAGAATGGACACTCTATATGTGTCCCTAAGCCAAGGTAGCAAGGTCTTTGGAGGAC
>Myh7_1
GCTCAGAGCTGTGTTTGGGAAGAAAGGGGATTTCAAACTAAACCCTGAGTCTGTTGCCTAGACACCGAGCAGTGAAGCTTCTATAGCTGGAAGAACAAGAACGAGGCTGGGTGCCAGCGTTGCTCCCGGGGCCTGCAGGGGAAGACAAGGTCTCTCCTGTCCTGTCCCTCTCTCCACTAGGAAGAACAAAGATTGCACCCACGGCTAGACAGAGGCCAGGTGGACCAGGCAGCCGTAGCCATATCATCTACAGCCCTGGGTAACCCTGGGAGGCTCAGGCCTTGCGCCTCGAAAATCTGCAGGGCAGCGCTAGAACAGGAAAGGGCTCTAAAGCAGGACCATGAGCAACTGGTCCTCCTCCCCAAACAGCTTTGGCATACTTCTTAGCATCCCTAGCCCTCCTCCCCTGATTGGGATCAACTTCCTATCTGCTG
I have made a fasta file listing the amplicons as the following, but it didn't work with Bismark. I got 0% CpG methylation and 99% CHH methylation. Is there anything wrong with my amplicon reference? Thank you!
>Myh6_1
AATAACTGAGGTAAGGGCCTGGGTAGGGGAGGTGGTGTGAGACGCTCCTGTCTCTCCTCTATCTGCCCATCGGCCCTTTGGGGAGGAGGAATGTGCCCAAGGACTAAAAAAAGGCCATGGAGCCAGAGGGGCGAGGGCAACAGACCTTTCATGGGCAAACCTTGGGGCCCTGCTGTCCTCCTGTCACCTCCAGAGCCAAGGGATCAAAGGAGGAGGAGCCAGGACAGGAGGGAAGTGGGAGGGAGGGTCCCAGCAGAGGACTCCAAATTTAGGCAGCAGGCATATGGGATGGGATATAAAGGGGCTGGAGCACTGAGAGCTGTCAGACAGAGATTTCTCCAACCCAGGTAAGAGGGAGTTTCGGGTGGGGGCTCTTCACCCACACCAGACCTCTCCCCACCTAGAAGGAAACTGCCTTTCCTGGAAGT
>Myh6_2
CCTCCCATCAGGAGTGGAGGGTTGCAGAGGGAGGGTAAAAACCTACATGTCCAAACATCATGGTGCACGATATATGGATCAGTATGTGTAGAGGCAAGAAAGGAAATCTGCAGGCTTAACTGGGTTAATGTGTAAAGTCTGTGTGCATGTGTGTGTGTCTGACTGAAAACGGGCATGGCTGTGCAGCTGTTCAGTTCTGTGCGTGAGGTTACCAGACTGCAGGTTTGTGTGTAAATTGCCCAAGGCAAAGTGGGTGAATCCCTTCCATGGTTTAAAGAGATTGGATGATGGCCTGCATCTCAGGGACCATGGAAAATAGAATGGACACTCTATATGTGTCCCTAAGCCAAGGTAGCAAGGTCTTTGGAGGAC
>Myh7_1
GCTCAGAGCTGTGTTTGGGAAGAAAGGGGATTTCAAACTAAACCCTGAGTCTGTTGCCTAGACACCGAGCAGTGAAGCTTCTATAGCTGGAAGAACAAGAACGAGGCTGGGTGCCAGCGTTGCTCCCGGGGCCTGCAGGGGAAGACAAGGTCTCTCCTGTCCTGTCCCTCTCTCCACTAGGAAGAACAAAGATTGCACCCACGGCTAGACAGAGGCCAGGTGGACCAGGCAGCCGTAGCCATATCATCTACAGCCCTGGGTAACCCTGGGAGGCTCAGGCCTTGCGCCTCGAAAATCTGCAGGGCAGCGCTAGAACAGGAAAGGGCTCTAAAGCAGGACCATGAGCAACTGGTCCTCCTCCCCAAACAGCTTTGGCATACTTCTTAGCATCCCTAGCCCTCCTCCCCTGATTGGGATCAACTTCCTATCTGCTG
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