Question on: Alignment

[JoeHansen4444]

        Start   End NBases  Ambigs  Polymer NumSeqs
Minimum:    0   0   0   0   1   1
2.5%-tile:  1   332 12  0   3   102345
25%-tile:   1   15422   333 0   4   1023446
Median:     1   15422   335 0   4   2046891
75%-tile:   1   15422   357 0   5   3070336
97.5%-tile: 15616   16273   357 0   6   3991436
Maximum:    16273   16273   384 0   8   4093780
Mean:   655 14695   313 0   4
# of unique seqs:   1386222
total # of seqs:    4093780

I did a summary.seqs after aligning my sequences using the silva reference file. I know it is not recommend but I am looking at the V3V4 region and customized the reference database starting with 9895 and ending with 26167. I was surprised that the alignment summary showed the start was 1 for most tiles and that the 97.5% tile had a start higher than the end of any other tile. After the alignment I did an aling.check to see how well it worked and received this message: your sequences are 16274 long, but your map file only contains 50001 entries. please correct. Could this be because the reference database is off making the alignment off or possibly a few bad sequences that are throwing the rest off? Any suggestions on how to fix this problem would be greatly appreciated.

[pschloss]

The file we use for align.check is based on the full 50000 column alignment so using the trimmed alignment would cause problems.

For screen.seqs you would want to use start=1, end=15422

Pat

[JoeHansen4444]

Thank you!