Closed flopezo closed 5 years ago
Hi, yes this should be possible. I give a short description at https://github.com/Oshlack/necklace/wiki/Options but let me know if you need further information. If you have mutiple fasta assemblies, you should combine them into a single fasta file and pass that as the de_novo_assembly_file parameter.
Hello, I am passing de novo assembly with the de_novo_assembly_file parameter, but Necklace still expects reads_R1 and reads_R2 to be provided. How to avoid this? best,
Mirella
You will still need to provide the read files. These are used for the genome-guided assembly (unless you also pass a pre-assembled .gtf file), and also used to obtain the read counts (which you can use for differential expression analysis) and for reporting some information about the superTranscriptome assembly.
Is possible to provide fasta reads? Thanks!
No, unfortunately not at this stage. But I'll keep it in mine for future versions!
Hello,
I was wondering if it is possible to pass de novo and genome-guided
Trinity
assemblies in FASTA format and aStringTie
assembly tonecklace
. I have pre-generated assemblies and am interested in using the recently addednecklace
optionsde_novo_assembly_file
andgenome_guided_assembly_file
.Any help is greatly appreciated!