I'm trying to align some Illumina amplicon sequencing, generated on a MiSeq, using Rsubread. It outputs .bam, .indel.vcf, and .summary files, but no .bai file, so I can't display the results in IGV. Here's how I got to this point:
Download the chr5.fa.gz reference sequence from UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/).
Create an index using:
Align my paired end sequencing files:
reads1.ch5 <- file.path(dirPath, "MSH3repeat_S1_L001_R1_001.fastq.gz")
reads2.ch5 <- file.path(dirPath, "MSH3repeat_S1_L001_R2_001.fastq.gz")
align(index="reference.ch5", readfile1=reads1.ch5, readfile2=reads2.ch5, output_file="alignResults.ch5.BAM")
How do I get it to make a .bai file, and how do I then display the results in IGV? Thanks!