can you help me?
I have to do analysis with the MiSeq SOP commands
I have only the foward file (R1_001.fasta) to do the analysis and I’m having trouble performing the summary.seqs, I’ll put down what I did.
1- convert fastaq files to fasta file
(fastq.info (fastq = file) it gave me 2 files [.fasta and .qual]
2- Create 2 groups
group 1
make.group (fasta = 01_R1_001.fasta-02_R1_001.fasta, groups = T1_1-T1_2) it gave me 1 group file, then renamed group1
group 2
[make.group (fasta = 01_R1_001.fasta-02_R1_001.fasta, groups = T2_1-T2_2) it gave me 1 group file, then renamed group2
3 - joined the groups to create a unique file
merge.files (input = group1-group2, output = file) it gave me a file [.file]
4- At this moment I have the problem, now I want to summarize.
summary.seqs (fasta = file) it reports the following message:
Using 4 processors.
[WARNING]: We found more than 25% of the bases in sequence 02526_121_000000000-BBCTW_1_1101_18573_2070 to be ambiguous. Mothur is not setup to process protein sequences.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 6463147 6327110 5918999 24 1
2.5% -tile: 1 6463147 6327110 5918999 24 1
25% -tile: 1 6463147 6327110 5918999 24 1
Median: 1 6463147 6327110 5918999 24 1
75% -tile: 1 6463147 6327110 5918999 24 1
97.5% -tile: 1 6463147 6327110 5918999 24 1
Maximum: 1 6463147 6327110 5918999 24 1
Mean: 1 6463147 6327110 5918999 24
of Seqs: 1
It took 1 secs to summarize 1 sequences.
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What am I doing wrong.
Thank you.