aligning with igblast

Question

[genya35]

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

[h.mon]

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.

[genya35]

i have no problem with running igblast, however, it's not returning this particular del as a match for J region. Thanks