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difficulty aligning to IGKdel reference #53

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HLAmolec opened this issue Jun 4, 2019 · 0 comments
Open

difficulty aligning to IGKdel reference #53

HLAmolec opened this issue Jun 4, 2019 · 0 comments

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@HLAmolec
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HLAmolec commented Jun 4, 2019

Hello,
I can't get igblast to call a del in J IGK gene from custom reference file I've made. It works with blastn but not igblast. Could you please suggest how tweak the parameters to get it to work?

reference:

IGKDEL
GGTACCTGAAGAATTTTCAGGATCAACATTTGTAAGCATTATCAGCCCAGGATAATGCTTATTTACAGCA
GTTCAACTTTTCTCACCTGCAGTAGTTTACTTTGATGAAATCCTGCTTATTTTTCACAATTAAAATTGCG
TCCATGGCCCTTGTTACCCTTAAGAATTATATTTTGCTGACACAATCTCTTTATCTACATTTCACCTAAG
TAAGCTTTTTCTTTACATGATTTTAAGTCATTTTCCAAAACAGAAAAGCATAATTATACAACCTTCTATG
TGTATTGGAGGAAAAAAAGGGTCACACAAATAATAGTACACTCTCTCAGTTAAGGAGTAGGCAGGAGGAG
GGGGTTGAGAAAGACAAACCAGAAAGAATTACATGAAATTTTCCTTCCTCCTCACTGAGCCTCCCTTGAA
TTGTCCAATAATATCCCCCCAACACACACACATAGACACAGAGCAGACTGTGAGGGACACGCAGCCTGGG
TGGGACTCCAGGAGCCAGCTCTTACCCTAGAGTTTCTGCACGGGCAGCAGGTTGGCAGCGCACACTGTGG
GAGCCCTAGTGGCAGCCCAGGGCGACTCCTCATGAGTCTGCAGCTGCATTTTTGCCATATCCACTATTTG
GAGTCTGACCTCCCTAGGAAGCCTCCCTGCTCCCTAGGACAACCTGCTCTGACCTCTGAGGACCTGTCTG
TAAACGTCCAGAGAAAAGCATGTGCCTGAAGGGTCTATGAAGGGGCTTGAGGCAAGTAGGGAGCCCAGCC
CAGCTAACATTTGCAGCCATGGGATGGCTTTGTGTACCTAGAAAAGCAAAGATGAGGACTAGGCGAGCAC
AGGCCCCAAACGTTCACGATACACATCTCACTGCAAAGAAATGTCCTCTGGCCACTTTATAATGCAGCTC
TAACTATAACTGGTGCTTTGCTGGTTTGTGGCCTGGGCTGGTCTCCCAGAGTCAGTGGCTTTGGGTGAGA
TGGCTCCAGGAGACAGCAGAAACTCTCATATATGAAGCCTTGCTTGCAGCGATTTGAGGCTTACTAGGGA
AAAGCCATGATGGGTTTTATAGAGCATTAACTGTGATACGCCATCTAGGGCTGAGAGCTC

Test sequence :
AGAGCCGCGGTCTTTCTCGATTGAGTGGCTTTGGTGGCCATGCCACCGCGCTCTTGGGGCAGCCGCCTTGCCGCTAGTGGCCGTGGCCACCCTGTGTCTGCCCGATTGATGCTGCCGTAGCCAGCTTTCCTGAGCCCTAGTGGCAGCCCAGGGCGACTCCTCATGAGTCTGCAGCTGCATTTTTGCCATATCCACTATTTGGAGTCTGACCTCCCTAGGAAGCCTCCCTGCTCCC

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