HLAminer RNA-seq vs Whole exome seq
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Entering edit mode
3.4 years ago
oghzzang ▴ 40

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. :>

RNA-Seq HLAminer HLA WXS • 1.4k views
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Entering edit mode
3.4 years ago
oghzzang ▴ 40

Maybe I found the solution.

As I said at my question, i can use identical pipeline.

Different part is only HLA reference file.

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