search

BackofenLab / GraphClust-2

A pipeline for structural clustering of RNA secondary structures
GNU General Public License v3.0
14 stars 4 forks source link

GraphClust-2 on RNA-seq data? #71

Closed mavino closed 3 years ago

mavino commented 3 years ago

Mine is a question and not an issue, I am very new to this area. I got a rich deepgen fastq data set (coming from rna-seq data) of an organism we know the reference genome but nothing about non coding RNA. I easily got a bam file out of it after quality control and alignment... is there any way I could use graph-clust-2 to detect and classify non coding RNA in the whole genome starting from the bam file? Will it make sense for my purpose to use your software? Thank you very much!

mmiladi commented 3 years ago

Hi @mavino ,

GraphClust2 can be used to classify ncRNAs. The baseline input would be fasta files, alternatively, you may start from region information (e.g., a BED file or GTF file) using auxiliary tools available in Galaxy. The tool is not designed for the purpose of separating ncRNAs from protein-coding RNAs. Best, -M

mavino commented 3 years ago

Thank you so much for the prompt and helpful answer!!