Troubleshooting the read mapping lab
Hey everyone! A few people are reporting some trouble in making this lab work so I updated all my software and went in. I am just going to walk through what worked with one sample. I started with the BC26 chloroplast file from SRA. This is fine: fastq-dump SRR1763773 Moved it to a shorter filename: mv SRR1763773.fastq BC26.fastq Built the bowtie2 index from the reference genome file. This is fine: bowtie2-build NC_007898.fasta NC_007898 This command should produce this output, including…