clustering sequence FASTA GSS, EST, Transcripts
I want to do clustering (k-means) and redundancy removal of my FASTA sequences which are mainly GSS, EST and assembled transcripts, to create a reference set for my short query sequences. My short query sequences can target either DNA or RNA. So I need some expert guidance. Also should I convert lower case base sequences into upper case for doing this task. Any suggestion would be highly appreciated.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Expert Guidance Required for De Novo Transcriptome Analysis
written by ben@f •
-
Maintaining the coverage filter in mmseqs for cascaded clustering
written by Victor •
-
K means clustering of expression data of different bacterial species using orthologous groups
written by Thomas •
-
Any tools that can score for alignment of two short sequences allowing ambiguous base
written by Zealseeker •
-
Phylogenetic analysis and Substitution rate calculation
written by SJ Basu •
-
"OID not found" error with GI-list and preformatted nt BLAST database
written by ziv84 •
-
eXpress uniq_counts estimation
written by useless_ulysses •
-
Cufflinks vs. Cuffcompare - number of assembled transcripts
written by wstfljs
-
Validation Of De Novo Rna-Seq Assembly
written by Pasta •
-
Blast Settings For Short Sequences
written by kevin.l.neff •
You might look at
dedupe.shfromBBTools. https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/dedupe-guide/You should also look at CD-HIT which is specifically tailored for this type of application and has specific subprograms.
Thanks for your answer genomax, but I have found uclust to be better than CD-HIT