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Hi @Sheila , Thanks for your reply. Hm, I'll try STAR and compare. Meanwhile, is it possible to ignore the NotPrimaryAlignmentFilter filter in GATK? Also, based on your experience, is it normal to have many secondary alignment in RNA-seq?
Hi @Sheila , alright thank you for you suggestion :)
Hi @Sheila , (Quote) Thank you for your reply. I use b38 as my reference (not b37) that I downloaded from Ensembl (Homo_sapiens.GRCh38.dna.primary_assembly.fa). Actually, I downloaded the VCF file from your resource bundle. Also I have checked your…
Hi, I am doing variant calling on RNA-seq and follow your RNA-seq best practice. Now, I am doing RealignerTargetCreator (before IndelRealignment). I performed HISAT2 for the alignment using HISAT2 built-in reference which use Ensembl gene annotatio…