Dear Biostars, Hi.
I have asked similar question but I have not received an acceptable answer or guideline, so I am asking it in other words :
Imagine that I have done a de novo transcriptome assembly from RNA-seq data using Trinity (no reference genome).
I have 3 biological replications for condition1 and 3 for condition2 (I have launched standart pipeline using RSEM and DESeq2 for DEG analysis)
1- is it practical to discover condition-dependent SNPs from this kind of RNA-seq project (non-model animals)?
2- if 1 = positive, How ? (please mention appropriate software or pipeline)
this is an example of SNP report in one paper:
Finally, a thorough genetic marker discovery pipeline led to the retrieval of 85,189 SNPs and 29,076 microsatellites enriching the available genetic markers for this species.
NOTE: almost each gene/transcripts in Trinity assembly has several isoforms