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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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2 votes
1 answer
140 views

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 ...
1 vote
1 answer
148 views

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 ...
3 votes
1 answer
149 views

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)...
1 vote
0 answers
195 views

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 ...
1 vote
1 answer
1k views

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 ...
2 votes
1 answer
208 views

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 ...
2 votes
0 answers
90 views

Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
1 vote
0 answers
195 views

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 ...
3 votes
3 answers
11k views

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 ...
2 votes
2 answers
80 views

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: ...
1 vote
1 answer
310 views

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 ...
2 votes
1 answer
423 views

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
1 vote
1 answer
2k views

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: ...
8 votes
3 answers
2k views

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 ...
2 votes
1 answer
106 views

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,...