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mafusa20
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@mafusa20-19278
Last seen 5.9 years ago
i'm do the pipeline of ASV for 16s analysis with demultiplexed files with .fq format.
> list.files(path)
[1] "DAtos demulteplixados.Rproj" "filtered"
[3] "Mock_S280_L001_R1_001.fastq" "Mock_S280_L001_R2_001.fastq"
[5] "SAMPLE1_1.fq" "SAMPLE10_1.fq"
[7] "SAMPLE11_1.fq" "SAMPLE12_1.fq"
[9] "SAMPLE13_1.fq" "SAMPLE14_1.fq"
[11] "SAMPLE15_1.fq" "SAMPLE2_1.fq"
[13] "SAMPLE3_1.fq" "SAMPLE4_1.fq"
[15] "SAMPLE5_1.fq" "SAMPLE6_1.fq"
[17] "SAMPLE7_1.fq" "SAMPLE8_1.fq"
[19] "SAMPLE9_1.fq" "silva_nr_v128_train_set.fa.gz"
[21] "silva_species_assignment_v128.fa.gz"
>fnFs <- sort(list.files(path, pattern="_1.fq", full.names = TRUE))
> sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 1)
> sample.names
[1] "SAMPLE1" "SAMPLE10" "SAMPLE11" "SAMPLE12" "SAMPLE13" "SAMPLE14" "SAMPLE15" "SAMPLE2"
[9] "SAMPLE3" "SAMPLE4" "SAMPLE5" "SAMPLE6" "SAMPLE7" "SAMPLE8" "SAMPLE9"
> plotQualityProfile(fnFs)
Error: record does not start with '@'
Help my please.