Mapping Illumina reads against one single gene Vs whole genome

Question

[praasu]

Hello,

I have mapped iclip-seq raw reads against single snRNA gene and whole genome (hg38) using Bowtie 2. I observed different alignment pattern in both case when I visualize in gbrowser the particular genes (snRNA gene). I would really appreciate if anybody has any suggestion and comments

Command used : bowtie2 -p 2 -N 1 -x base_name -U CLIP_raw_reads.fq

[GenoMax]

Aligning to a reduced representation of genome (if your data came from full genome) is always going to cause discrepancies as by default aligners will try to do their best to align data.

[praasu]

Thank you very much for your answer. Yes, the data is from the whole genome. If I understand correctly, aligning whole genome ICLIP-seq data to a single gene is not an appropriate way to do that. So, I should only trust to alignment obtained from ICLIP-data aligned to whole genome (hg38) reference?

Answer 1

[h.mon]

Bowtie2 will consider as mapped all reads with alignments to the reference above a certain score, and will output the best alignment that passes this score, even if the alignment is imperfect. When you use the sequence of a single gene as reference, reads that would otherwise map elsewhere in the genome with a higher score, will be mapped to this single gene and will be considered the "correct" alignment as their score is above the threshold.