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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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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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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3 votes
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Does cutadapt trim trailing N's first and then use max_n to filter reads?

Background I want to trim leading and (likely just) trailing N's from my WES (Illumina NextSeq500) reads with cutadapt (--trim-n)...
Dandelion's user avatar
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Why don't all reads have adaptors?

I got NGS reads back from sequencing platform. I check for adaptors and trimmed them. But I realized only a fraction (eg 30%) have adaptors... why not all of them? Thanks
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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,...
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When using cutadapt, can I specify an R2 adapter as optional when I have a required R1 adapter?

I'm using cutadapt 3.5 to trim adapters and perform some filtering on paired-end data. Both R1 and R2 sequences have 3' adapters that might be found depending on the sequence length, but R1 also has ...
Jesse's user avatar
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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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2 answers
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Error after trimming illumina adapters

I am removing illumina adapters of the NGS data with a loop. My NGS data is storage in /data/HTS_seq/. I used this function: ...
Adrián P.L.'s user avatar
2 votes
1 answer
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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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1 answer
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How to identify index sequences for cutadapt for atac-seq

I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads. I am following the galaxy ...
Faleevs's user avatar
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1 vote
1 answer
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processing multiple fastq files with cutadapt

I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command ...
Amit'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 ...
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Searching for adapter sequences in FASTQ files - metgenomics

I have recently received some metagenomic data from 16S rrna sequencing. The sequencing company claim to have removed primers, however not adapter sequences. Please note that the files have been ...
h3ab74's user avatar
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1 vote
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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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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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