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Questions tagged [cutadapt]

A command-line tool used to remove adapter sequences from raw sequencing reads. Can also be used to trim low-quality bases from the ends of reads.

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Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
justinian482's user avatar
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working with cutadapt

I'm working with ion torrent data where I apply the program cutadapt. I'm analyzing ITS seq data, as well as Matk. When I'm using cutadapt, I search the information for this genes, and built new ...
Sofia's user avatar
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Removing adapters + primers from fastq files

I am currently in the process of removing adapters and primers from some 16S data acquired, and have a conceptual question regarding this pre-processing step: So there are a series of different primer ...
h3ab74's user avatar
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Why is cutadapt discarding some paired end reads?

So, I am using cutadapt to remove two primers from some paired end reads. I have 2 files for each sample, i.e. sample_R1.fastq and sample_R2.fastq. I have primer_1 and primer_2 and both of them can be ...
gabt's user avatar
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