im new in this matter. and read some papers and watch some tutorial videos. i am in the way of aligning my dara. but in igv my data dosent match with my reference genome even iv got 92.7 % overal alignment with hisat2. some one help me pz
Both reference genome in fasta format and mapped reads file in bam format need to be indexed, and the bam file needs to be sorted as well. For the fasta reference:
samtools faidx ref.fasta
For the mapped bam:
samtools sort -o sorted.bam mapped.bam samtools index sorted.bam
In addition, the reference genome loaded into OGV need to be the same used for mapping.