I am working on homosapien chipset data I have done the indexing using the bowtie2 tool of the top-level assembly from the ensemble website, https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_rm.toplevel.fa.gz
Now while doing the alignment using bowtie2 I am getting a very low overall alignment rate like 35%, 39% for all the samples. Why is the alignment rate so low? Any suggestions on what am I doing wrong or what is causing that ?? and what can I do for better results I am new to bioinformatics so kindly bear if this is a very basic question but any advice/help is appreciated.
Following is the code for indexing
bowtie2-build input.fasta genome_index
for alignment :
bowtie2 -p 12 -q -x genome_index -U my_inputfile -S my_output
Any help would be appreciated.
Thanks Regards Mehvi