Need a piece of advice for microbiome data
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7.2 years ago
unique379 ▴ 110

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.

microbiome MiSeq • 1.4k views
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It looks like your paired-end reads were merged at a upstream step which resulted in longer contigs.

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