Update clustering method
In my faculty, we use ion torrent. After the trimming and fastq analysis, we perform clustering with usearch based on the identity of the reads length. However, I want to know if there is a new way to perform clustering. I'm sorry if this is a not so interesting question. Thanks
• 1,004 views
•
link
written
by
anasofiamoreira94
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Reference genome for RNAseq analysisin Galaxy
written by Gracious •
-
What is the current recommended way to process/ analyze Ion Torrent Proton RNAseq data
written by cwwong13 •
-
pipeline for variant discovery in target resequencing
written by sarastrafella.ss •
-
can I use ion torrent fastq in illumina pipeline?
written by emawhitt •
-
Ion torrent errors in fastq
written by anasofiamoreira94
-
ion torrent pipeline
written by acebolladaso.iacs •
-
Differences of reads between uBam and fastq from Ion Torrent
written by anasofiamoreira94
-
Length of reads in a RNAseq experiment
written by Carlos Caicedo
-
Simulating single end reads with dwgsim
written by kautilya
-
Max Length With Fastx Tookit
written by serpalma.v •
What are you clustering? Please add details.
I assume you are clustering reads to identify sequence duplicates. Take a look at
clumpify.shand its features here: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates. If some of reads are expected to be shorter (i.e contained in others) then you will need to usecontainment=toption.I will see your suggestion @genomex, thanks!