No results generated for HLA samples

cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

https://cfe-lab.github.io/MiCall

GNU Affero General Public License v3.0

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No results generated for HLA samples #6

Closed ArtPoon closed 10 years ago

ArtPoon commented 10 years ago

Because we have no HLA-A, -B, or -C references in csf2counts This is tricky because there is no meaningful reading frame - the region being sequenced comprises two exons separated by an intron.

ArtPoon commented 10 years ago

Created new driver STEP_5_CSF2NUC.py that takes nucleotide reference sequences and trims CSF reads, outputs alignment (Amplicon mode only!)