Hi All,
I am following Miseq SOP to treat V3-V4 2*300 raw data with the initial make.contigs(ffastq=f1.fastq,rfastq=r1.fastq) command. But I get some short reads with only ~50 bp .I am wondering this normal for the V3-V4 data, or I made some mistakes in the command.
Thanks
mothur >
make.contigs(ffastq=17.fastq,rfastq=17-1.fastq,processors=4)
Using 4 processors.
Making contigs…
Done.
It took 34 secs to process 72348 sequences.
Output File Names: 17.trim.contigs.fasta 17.scrap.contigs.fasta 17.trim.contigs.qual 17.scrap.contigs.qual 17.contigs.report
[WARNING]: your sequence names contained ‘:’. I changed them to ‘_’ to avoid problems in your downstream analysis.
mothur >
summary.seqs(fasta=17.trim.contigs.fasta)
Using 4 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 35 35 0 2 1
2.5%-tile: 1 39 39 0 3 1809
25%-tile: 1 42 42 0 4 18088
Median: 1 58 58 0 5 36175
75%-tile: 1 465 465 0 6 54262
97.5%-tile: 1 465 465 3 13 70540
Maximum: 1 601 601 252 188 72348
Mean: 1 240.971 240.971 0.500387 5.38984
of Seqs: 72348
Output File Names:
17.trim.contigs.summary
It took 1 secs to summarize 72348 sequences.