I did combine them at the make. contigs stage and used the silva to cover the v3 and v4 regions and the miseq got filtered out.
Can you post the output of running summary.seqs with both sets of data together? Do all of the data cover the v3-v4 region? It’s possible the MiSeq data isn’t as good as the NextSeq
Pat
it showed the same as what i showed for the nextseq summary above
Can you post the output of running summary.seqs on the MiSeq and NextSeq data separately?
Pat
for the nextseq data,
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 35 35 0 2 1
2.5%-tile: 1 37 37 0 4 34651
25%-tile: 1 440 440 0 4 346502
Median: 1 460 460 0 5 693003
75%-tile: 1 465 465 0 6 1039504
97.5%-tile: 1 466 466 2 7 1351355
Maximum: 1 602 602 61 301 1386005
Mean: 1 428 428 0 5
for the miseq data,
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 248 248 0 3 1
2.5%-tile: 1 252 252 0 4 1185
25%-tile: 1 253 253 0 4 11845
Median: 1 253 253 0 4 23689
75%-tile: 1 253 253 0 5 35533
97.5%-tile: 1 253 253 5 6 46193
Maximum: 1 501 501 64 151 47377
Mean: 1 253 253 0 4
of unique seqs: 47377
total # of seqs: 47377
It appears to me that your MiSeq data are V4 and your NextSeq data are V4-V5. When you run screen.seqs using start and end coordinates for V4-V5 you will lose all of the MiSeq data. You need to analyze the datasets separately.
Pat
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