I am working on Ribo-seq analysis workflow and the sample that I am using is a paired end sample, so when I do the pre-processing steps like fastqc, trimming then postqc , the results I am getting are not good quality maybe because the sample is paired end and paired end samples get overlapped while processing, then I tried with only one read and the results I got were good quality results. So, for Ribo-seq profiling can we use single reads or the paired end is required? I reviewed some literature also on this, and in many papers single end processing is being carried out
•
written
by
mansiparihar13 •
1 answer
Yes, single-end reads are sufficient and widely used for Ribo-seq profiling, as ribosome footprints are typically short (~26–34 nt), making paired-end sequencing unnecessary for most analyses. Many pipelines (e.g., nf-core/riboseq) support both, but single-end avoids overlap issues in short fragments and is routine in literature. Stick with your single-end results—they're valid. If needed, tools like Trimmomatic with PE mode and overlap handling can fix paired-end QC.
Kind regards, Kevin
Log in to answer this question.
-
Ribo-seq Trimming Issue: Massive Read Loss in Paired-end Mode
written by Sammy •
-
SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
written by Dhatri Badri •
-
Batch effect removal for RNA-seq data (single-end and pair-end)
written by hanny •
-
FastQC for paired end data
written by Dk •
-
quality control (ribo-seq)
written by andreiareis1987 •
-
Several failures present in QC of RNA-seq data from company via fastqc
written by citronxu •
-
Filtering and Trimming Metagenomic Data
written by MK2000 •
-
Why does read quality drop after adapter trimming with cutadapt?
written by Nabeel Ahmed •
-
Paired-end RNA Seq data: How to deal with unpaired data after trimmomatic
written by aggregatibacter
-
Trimming read length & quality in a FASTQ file
written by ChIP
