If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?