Tweet
Hi everyone. I have to analyze some paired end reads coming from a Illumina MiSeq experiment. What I want to do is removing duplicate reads that not only have the same start-end coordinates but also have 100% sequence identity. Is there any tool that can help me do that? I want to work with BAM files not with FastQ files. Thanks!
-
-
If sequences have 100% identity then they should have the same mapping coordinates, so there's no reason to work with bam files in this case. I wrote a program that can do this for fastq, but not for bam:
dedupe.sh in=reads.fq out=deduped.fq ac=f t=1
There should be tools that can do so on bam files by sorting by sequence, but I don't know what they are offhand.
-
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM -
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM
Comment