Question: HLAminer RNA-seq vs Whole exome seq
0
gravatar for oghzzang
19 months ago by
oghzzang40
oghzzang40 wrote:

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 hla hlaminer wxs • 730 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by oghzzang40
0
gravatar for oghzzang
19 months ago by
oghzzang40
oghzzang40 wrote:

Maybe I found the solution.

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

Different part is only HLA reference file.

ADD COMMENTlink modified 19 months ago • written 19 months ago by oghzzang40
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2051 users visited in the last hour