Problem in execuation of filterAndTrim command in DADA2
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abhisek001 • 0
@6d5973d2
Last seen 16 days ago
India

Hello scientific community... I was running the following command "filterAndTrim" with default parameters for trimming of 16s data in DADA2 pipeline it worked fine. The only problem I have is that it is trimming more than 95% of my reads for all samples why it is happening can anyone tell?

My Fastaq files are taken without any trimming into third-party software like cutadapt, fastp or trimmomatic. If all the reads are got trimmed how can I proceed with so little reads. Any guidance? I also tried to cut the bad sequences from the end of the sequence then most of the reads were filtered out.

out <- filterAndTrim(dataF, filt.dataF, dataR, filt.dataR, truncLen=0,
                     maxN=0, maxEE=Inf, truncQ=2, rm.phix=TRUE,
                     compress=FALSE, multithread=FALSE)

head(out) -

                    reads.in reads.out
AIJ_R1.fastq    63023      1565
AIZ_R1.fastq   104880      2593
AOJ_R1.fastq    76768      2029
AOZ_R1.fastq    75343      1866
FIJ_R1.fastq      68518      1615
Bioconductor dada2 • 166 views
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This problem was solved when I used trimmed sequenced with fastp and used those sequences on DADA2. Raw reads can not give the desired result. Thanks.

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