I used a VCF file to generate a consensus haploid reference genome. Then, I mapped the RNA-seq reads to the reference. I found the output bam file only showed correctly transformed coordination on the 1st chromosome in the reference. All the other chromosome showed wrong coordination. This impedes the following analyses, including using FeatureCounts. Do people experience the similar thing?
I used a VCF file to generate a consensus haploid reference genome. Then, I mapped the RNA-seq reads to the reference. I found the output bam file only showed correctly transformed coordination on the 1st chromosome in the reference. All the other chromosome showed wrong coordination. This impedes the following analyses, including using FeatureCounts. Do people experience the similar thing?
The script I used is attached below: