Hi,
I have an eland result file. For number 1, 2, and 4 reads, there are N at the first position. However alignment result still has U0, why? How does eland decide the match position on chr? For the last read, I blasted it against human genome on NCBI, which showed the match position from 8006331 to 8006364. Why are they different?
TIA,
litd
>HWI-EAS344:4:1:0:1037#0/1 NGGGGAGAATCTGTTTCCTTGCTGTTCTGCTTCTG U0 1 0 0 chr15.fa 37949556 F DD
>HWI-EAS344:4:1:0:757#0/1 NAGACATCGGCTGCAGGCTATGACCACCCGCTCTT U0 1 0 0 chr14.fa 98886375 F DD
>HWI-EAS344:4:1:0:2002#0/1 NATCCCAGCCACTCAGGAGGCTGAGGCAGGAGAAT R0 255 255 255
>HWI-EAS344:4:1:0:1129#0/1 NTTAAGAATTAACCTGTGAATTTTTGAAGAAGGCA U0 1 0 0 chr5.fa 57447729 F DD
I have an eland result file. For number 1, 2, and 4 reads, there are N at the first position. However alignment result still has U0, why? How does eland decide the match position on chr? For the last read, I blasted it against human genome on NCBI, which showed the match position from 8006331 to 8006364. Why are they different?
TIA,
litd
>HWI-EAS344:4:1:0:1037#0/1 NGGGGAGAATCTGTTTCCTTGCTGTTCTGCTTCTG U0 1 0 0 chr15.fa 37949556 F DD
>HWI-EAS344:4:1:0:757#0/1 NAGACATCGGCTGCAGGCTATGACCACCCGCTCTT U0 1 0 0 chr14.fa 98886375 F DD
>HWI-EAS344:4:1:0:2002#0/1 NATCCCAGCCACTCAGGAGGCTGAGGCAGGAGAAT R0 255 255 255
>HWI-EAS344:4:1:0:1129#0/1 NTTAAGAATTAACCTGTGAATTTTTGAAGAAGGCA U0 1 0 0 chr5.fa 57447729 F DD