Dear biostar users.
Hello I'm using HLAminer.
Can I use identical HLAminer pipeline for RNA-seq inputs and DNA-seq inputs? I only changed HLA reference file(RNA seq : CDS file, DNA seq : GEN file).
The basis of this is this journal "Derivation of HLA types from shotgun sequence datasets" In The journal said " HLA coding DNA sequence (CDS) and genomic sequence databases from release 3.3.0 and 3.4.0 were obtained, respectively, from [21]. HLA-I exon 2 and 3 concatenated sequence FASTA files were prepared using exon coordinates available from the flat file database (EMBL format) released by IMGT [22]. For HLA allele predictions from RNA-Seq data, we used concatenated exons 2 and 3 as sequence targets for assembly using the TASR assembly tool [23]. For predictions from genome and exome NGS data, we used HLA-I genomic sequences from major genes A, B and C."
So, when I use HLAminer, I only changed inputs (RNA seq or WXS) and HLA reference file (RNA seq : CDS file, DNA seq : GEN file).
Is it right?
Thank you so much. :>
