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bsb-mothur [2018/02/15 03:15]
telatina
bsb-mothur [2018/02/15 03:21] (current)
telatina
Line 53: Line 53:
 MiSeq   ​MiSeq_SOP/​F3D143_S209_L001_R1_001.fastq MiSeq_SOP/​F3D143_S209_L001_R2_001.fastq MiSeq   ​MiSeq_SOP/​F3D143_S209_L001_R1_001.fastq MiSeq_SOP/​F3D143_S209_L001_R2_001.fastq
 ... ...
 +</​code>​
 +==== Merge paired reads ====
 +From now on, Mothur is running from the MiSeq_SOP directory. Fusing the commands will require the [[https://​mothur.org/​wiki/​Make.contigs|make.contigs]] command:
 +<​code>​
 +make.contigs(file=mapping.files,​ processors=8)
 +</​code>​
 +==== Summary ====
 +<​code>​
 +summary.seqs(fasta=mapping.trim.contigs.fasta)
 +</​code>​
 +
 +<​code>​
 +Using 4 processors.
 +
 +                Start   ​End ​    ​NBases ​ Ambigs ​ Polymer NumSeqs
 +Minimum: ​       1       ​248 ​    ​248 ​    ​0 ​      ​3 ​      1
 +2.5%-tile: ​     1       ​252 ​    ​252 ​    ​0 ​      ​3 ​      3810
 +25%-tile: ​      ​1 ​      ​252 ​    ​252 ​    ​0 ​      ​4 ​      38091
 +Median: ​        ​1 ​      ​252 ​    ​252 ​    ​0 ​      ​4 ​      76181
 +75%-tile: ​      ​1 ​      ​253 ​    ​253 ​    ​0 ​      ​5 ​      ​114271
 +97.5%-tile: ​    ​1 ​      ​253 ​    ​253 ​    ​6 ​      ​6 ​      ​148552
 +Maximum: ​       1       ​502 ​    ​502 ​    ​249 ​    ​243 ​    ​152360
 +Mean:   ​1 ​      ​252.811 252.811 0.70063 4.44854
 +# of Seqs:      152360
 +
 +Output File Names:
 +mapping.trim.contigs.summary
 </​code>​ </​code>​