Entering edit mode
7.6 years ago
unique379
▴
120
Dear folks,
I am new to analyze for micro biome data. I am trying to use mothur for my analysis. I have MiSeq paired (fastq) microbiome data. After using contigs and summary.seqs command i need to screen the sequences from my reads. The sumary file look like this:
mothur > summary.seqs(fasta=stability.trim.contigs.fasta)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 35 35 0 3 1
2.5%-tile: 1 290 290 0 4 98245
25%-tile: 1 458 458 0 4 982449
Median: 1 460 460 1 6 1964897
75%-tile: 1 465 465 4 6 2947345
97.5%-tile: 1 466 466 22 7 3831548
Maximum: 1 602 602 59 289 3929792
Mean: 1 450.165 450.165 3.55126 5.35893
# of Seqs: 3929792
Output File Names:
/Users/Destiny/Desktop/MicroBiome/OurData/stability.trim.contigs.summary
This point i need to select my minimum and maximum length in order to run screen.seqs but seeing summary output i am confused to select these lengths due to i read that microbiome reads supposed to have 250-300 bp and here i am seeing maximum length is about 600bp. please help.
It looks like your paired-end reads were merged at a upstream step which resulted in longer contigs.