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best practices for calling snps from RNAseq reads mapped to denovo transcriptome

Dear GATK community,
I would like to use GATK to call SNPs from RNAseq reads (from 7 libraries) mapped to a de novo transcriptome assembly (no reference genome available). I am having trouble finding best practices for the mapping rna-seq to a reference transcriptome. If best practices already exist, would someone let me know where to find them?

Since there is no reference genome, I don't think the STAR aligner is appropriate. For a previous investigation of assembly quality, I mapped each library to the assembly using Bowtie (not bowtie2). So, I already have for each library a file called "bowtie_out.coordSorted.bam", and a bunch of other files which I assume are index files for the reference (target1...4.ebwt, target.fa, target.fa.fai). Would it be reasonable to use these .bam files for downstream SNP calling in GATK? What are the specific steps I would need to take in order to do that?

Many thanks.
Caroline Judy



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