Give option to process illumina data.

sheffield-bioinformatics-core / periscope

A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.

GNU General Public License v3.0

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Closed mattdmem closed 4 years ago

mattdmem commented 4 years ago

How does amplicon assignment work
How to deal with paired reads
ORF assignment should still work
bwa mem mapping (-Y to softclip rather than supplementary alignments) bwa mem -Y -t 2 nCoV-2019.reference.fasta *.fastq.gz | samtools sort | samtools view -bh > illumina.bam

mattdmem commented 4 years ago

option now exists to process illunima data - normalisation still in progress