I did ChIP-sequencing. During sequencing process, one base was not called due to a problem at the 13 cycle of sequencing.
For Example, CTTCCTGGCCTGNTGCCCCTTGAGGACTCCCAGGTTAGTCCCTGGGCTAGA You can see it “N” at the 13th base.
I map this data using Bowtie and very few sequence was aligned.
I thought if I permit more number of mismatch sequence it would increase mapping.
I tried to change one of parameter in Bowtie : "Maximum number of mismatches permitted in the seed" from 2 to 3, but it did not work well.
How could I increase mapping with this sequencing data?
Si Ho Choi