search

Oshlack / necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis
https://github.com/Oshlack/necklace/wiki
GNU General Public License v3.0
21 stars 5 forks source link

Passing a genome-guided Trinity assembly to necklace #2

Closed flopezo closed 5 years ago

flopezo commented 6 years ago

Hello,

I was wondering if it is possible to pass de novo and genome-guided Trinity assemblies in FASTA format and a StringTie assembly to necklace. I have pre-generated assemblies and am interested in using the recently added necklace options de_novo_assembly_file and genome_guided_assembly_file.

Any help is greatly appreciated!

nadiadavidson commented 6 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.

MFlores2021 commented 6 years ago

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

nadiadavidson commented 6 years ago

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.

MFlores2021 commented 6 years ago

Is possible to provide fasta reads? Thanks!

nadiadavidson commented 6 years ago

No, unfortunately not at this stage. But I'll keep it in mine for future versions!