aligning with igblast
Hello,
I'm having a difficult time aligning the following sequence of IGK gene to a reference using igblast. It works with other tools but I must use igblast since it's part of the pipeline. Could someone please suggest how to tweak the parameters to get it to align?
Thanks
>test_sequence
AGAGCCGCGGTCTTTCTCGATTGAGTGGCTTTGGTGGCCATGCCACCGCGCTCTTGGGGCAGCCGCCTTGCCGCTAGTGGCCGTGGCCACCCTGTGTCTGCCCGATTGATGCTGCCGTAGCCAGCTTTCCTGAGCCCTAGTGGCAGCCCAGGGCGACTCCTCATGAGTCTGCAGCTGCATTTTTGCCATATCCACTATTTGGAGTCTGACCTCCCTAGGAAGCCTCCCTGCTCCC
reference:
>IGKDEL
GGTACCTGAAGAATTTTCAGGATCAACATTTGTAAGCATTATCAGCCCAGGATAATGCTTATTTACAGCA
GTTCAACTTTTCTCACCTGCAGTAGTTTACTTTGATGAAATCCTGCTTATTTTTCACAATTAAAATTGCG
TCCATGGCCCTTGTTACCCTTAAGAATTATATTTTGCTGACACAATCTCTTTATCTACATTTCACCTAAG
TAAGCTTTTTCTTTACATGATTTTAAGTCATTTTCCAAAACAGAAAAGCATAATTATACAACCTTCTATG
TGTATTGGAGGAAAAAAAGGGTCACACAAATAATAGTACACTCTCTCAGTTAAGGAGTAGGCAGGAGGAG
GGGGTTGAGAAAGACAAACCAGAAAGAATTACATGAAATTTTCCTTCCTCCTCACTGAGCCTCCCTTGAA
TTGTCCAATAATATCCCCCCAACACACACACATAGACACAGAGCAGACTGTGAGGGACACGCAGCCTGGG
TGGGACTCCAGGAGCCAGCTCTTACCCTAGAGTTTCTGCACGGGCAGCAGGTTGGCAGCGCACACTGTGG
GAGCCCTAGTGGCAGCCCAGGGCGACTCCTCATGAGTCTGCAGCTGCATTTTTGCCATATCCACTATTTG
GAGTCTGACCTCCCTAGGAAGCCTCCCTGCTCCCTAGGACAACCTGCTCTGACCTCTGAGGACCTGTCTG
TAAACGTCCAGAGAAAAGCATGTGCCTGAAGGGTCTATGAAGGGGCTTGAGGCAAGTAGGGAGCCCAGCC
CAGCTAACATTTGCAGCCATGGGATGGCTTTGTGTACCTAGAAAAGCAAAGATGAGGACTAGGCGAGCAC
AGGCCCCAAACGTTCACGATACACATCTCACTGCAAAGAAATGTCCTCTGGCCACTTTATAATGCAGCTC
TAACTATAACTGGTGCTTTGCTGGTTTGTGGCCTGGGCTGGTCTCCCAGAGTCAGTGGCTTTGGGTGAGA
TGGCTCCAGGAGACAGCAGAAACTCTCATATATGAAGCCTTGCTTGCAGCGATTTGAGGCTTACTAGGGA
AAAGCCATGATGGGTTTTATAGAGCATTAACTGTGATACGCCATCTAGGGCTGAGAGCTC
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What is a hard time? You failed to install and / or configure IgBLAST? Or is IgBLAST segfaulting or throwing any other kind of error message? Or you don't know how to use its command-line options? Or IgBLAST is running but its results are meaningless / strange?
Please explain how you are trying to run the tool, what do you mean by "hard time", and which are the error messages, if any.
i have no problem with running igblast, however, it's not returning this particular del as a match for J region. Thanks