How to do the downstream analysis in the non-genome species

[catslu]

Hi! Thanks so much for this package.

I am working some rna-seq in the maine species without genome

Your guide presents all downstream analysis example and R scripts with genome index, so how to work splash on the non-genome rna-seq.

[roozbehdn]

Hi catslu,

Yes, the provided R scripts for downstream analysis could be used when there are reference genomes for the input data (e.g., human or mouse data). When data does not have reference genome or it is metagenomics. One potential downstream analysis is to append anchor and target sequences to get extendors (each extendor is an anchor sequence + one of its target sequences) and then align these linger sequences to databases such as BLAST or PFAM to obtain more information about the detected sequences (to see if they contain functional protein domains or could be mapped to any ref sequences in BLAST database) and then you could proceed from there depending on the specific question you are interested in answering using your data and splash-called sequences.