I've the following problem. I'm using HISAT2 and Bowtie. I'm using a gene with 1200 nucleotides which is present in the hg38. When aligning my FASTQ data that ist around 250 nucleotides to the hg38 I get 99%+ mapping on the that gene, when I use the gene itself as a FASTA genome for mapping I get 0% mapping. The reads are all in-between those 1200 bases and if I run a blast on some of the reads I've a 100% match. Can someone explain to me what I'm doing wrong?
I can see that the script recognized the gene that I'm using as a genome:
@SQ SN:HPD_xdna_1182 LN:1182
There seems to be the issue?! Even if I rename it.
Dataset peek HISAT2 summary stats:
Total reads: 86715 Aligned 0 time: 86715 (100.00%) Aligned 1 time: 0 (0.00%) Aligned >1 times: 0 (0.00%)