Hi all,

I'm trying to test ATAC-seq data through ATACseqQC, first download SRR891278, which then transfer to sam file use bwa mem, and then tranfer to bam file use samtools view and samtools sort, but get an error below.

> bamfile <- '/simm/huangyulab/liufei/test/atac-testdata/SRR891278.1.sort.bam'
> bamQC(bamfile, index = '/simm/home/liufei/alignment_exercise/633_hs_genome_hs38d1.fa',outPath='/simm/huangyulab/liufei/test/atac-testdata/test_data/')
    Error in value[[3L]](cond) :
      failed to open BamFile: failed to load BAM index
      file: /simm/home/liufei/alignment_exercise/633_hs_genome_hs38d1.fa

I want to ask how can I get the index file and should that be a bam file?

Thanks

Use Rsamtools::indexBam() or from the command line samtools index ... on your sorted bam file.