Hi all,
I'd like to share a modular and transparent bash-based pipeline I’ve developed for pre-processing ddRADseq Illumina paired-end...
25 results in 0.0030 seconds.
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Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and de-duplication using cutadapt
Last edited by rafalwoycicki; 04-23-2025, 06:10 AM. -
Cutadapt Demultiplex
Hi all,
I'm working in R and trying to demultiplex some data using cutadapt
I have three files:barcodes.fastq.gz (which I have... -
Stuck at adapter trimming
Hi!
So, I'm trying to analyse and subsequently map the data deposited with the following paper:
http://science.sciencemag.o... -
Merging fastQ files and trimming advice
Hello everyone,
I am new to using NGS techniques and the bioinformatics tools for analysing the acquired data so I hope I can get some... -
Cutadapt trimming issues
Hi, perhaps someone could advise me on the following issue.
I was trimming my paired-end reads with cut adapt using the following command:... -
Why mapping rate is low after adapter trimming paired-end data?
I have the pipeline with the following trimming and mapping parameter:
...Code:trim_galore --stringency 5 --dont_gzip --trim1
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PLEASE HELP!!!! cutadapt 1.12 paired-end trimming: too many parameters
Hi,
I am trying to run paired end trimming with cutadapt 1.12 so STAR aligner won't complain that the two read files are not the same,... -
Demultiplexing PacBio sequences
Hi all,
I have the following problem:
I have a dataset containing circurlarized and linear DNA. It was amplified with two pairs of primers... -
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trim_galore - when to stop trimming?
I've just used trim_galore (arguments below) to trim the adapter sequences off of fastq files from Illumina hiseq 4000 run TruSeq prep. Cutadapt seemed... -
Cutadapt, list of adapter
Hello,
I am using Cutadapt, but I have a problem: It doesn't find adapter, but with a banal research with function "find" in... -
Problem in Using Tophat with Cutadapt output
I have fastq reads represented in SOLiD format (Reads are stored in two files, one in fasta format for reads, and another one contains qualities). here... -
Trying to remove nextera transposase sequence using cutadapt and fastqc
Hello everybody,
We just launched a nextseq500 run recently.
I analyzed it with Fastqc and I obtained an error at the adapter content...Last edited by ClemBuntu; 01-21-2015, 08:04 AM. -
STAR with trimmed reads
Hi Everyone,
I am doing a comparison of tophat2 vs STAR alignment of my RNA-seq data, and trimmed vs untrimmed data. (I was getting different... -
TopHat, trimmed PE reads, and SAM flags
Hi All,
I used cutadapt to trim my PE reads and TopHat to map the trimmed ones. TopHat could map most of them. Then I wanted to use HTSeq-Count...
