Tweet
I MiSeqed heterogeneous templates amplified via rolling cycle amplification (RCA) by a specific 6-nt primer. PE reads were merged into single ones around 500 nt. As a consequence of RCA, some of them consist of 100-200 nt repeats from short-size templates. Is anyone aware of tools that can process, extract, and consensus these kinds of reads? Many thanks.
-
-
You could take an example sequence and then use "bbduk.sh" from BBMap suite in filter mode to extract reads containing that sequence with "literal=sequence_you_want" option. Guide to use bbduk is here. -
I believe that is what I want. Thanks!Comment
-
GenoMax: Can I extract/separate reads with 0, 1, or 2 motifs (the motif is the same)? Could BB scripts do this job?Comment
-
Possibly. You will have to play with parameters for bbduk.sh. "0" should be easy to get.Comment
-
Okay, I will try. ThanksComment
-
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 on Modified Bases...Yesterday, 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