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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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 ...
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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)...
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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 ...
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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 ...
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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 ...
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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:
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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
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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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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,...
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