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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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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 ...
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removing nextera transposase adapters, cutadapt

I am learning about NGS analysis and im currently learning about QCing and removing adaptors. I am working on SRR1972920_1.fastq file. When running fastqc tool on that file, adapter contamination ...
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for loop cutadapt for files on a single directory

I have a bigfolder where i have a lot of fastq.gz files and I want to remove the adapters from all of them. I am trying then the following loop: ...
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Why does cutadapt remove low quality bases from the ends of reads only?

I use cutadapt to remove low quality bases from my Illumina reads. The algorithm only removes low quality bases from the end until it reaches a good quality base. If there is a bad quality base beyond ...
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efficient counting of dinucleotides/trinucleotides on fastq reads?

What's an efficient way of counting of dinucleotides/trinucleotide pattern on fastq.gz file reads? I know there are tools like seqtk that will be very efficient at reading through the .fastq.gz files,...