Originally posted by Rui
View Post
-
I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.Leave a comment:
-
samtools manual says they are " ’>’ or ’<’ for a reference skip".
Leave a comment:
-
mpileup format
I am using samtools mpileup to analyze my data, and have several lines like this:
chr1 14976 G 5 <<><> HHHHH
chr1 14977 C 5 <<><> HHHHH
chr1 14978 C 5 <<><> HHHHH
chr1 14979 T 5 <<><> HHHHH
chr1 14980 C 5 <<><> HHHHH
chr1 14981 A 5 <<><> HHHHH
chr1 14982 T 5 <<><> HHHHH
chr1 14983 G 5 <<><> HHHHH
chr1 14984 A 5 <<><> HHHHH
What are those ">" "<" or "*" mean in the reads base column? According to the description of the format (http://samtools.sourceforge.net/pileup.shtml), they should be only in the base qualities columns.
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Leave a comment: