Mapping reads to a very small reference

Question

[victoriahristovaa]

Hello!

I have two short genomic sequences, ~2700 bases each. I want to map short reads (Illumina TruSeq paired-end reads) to each of the ~2700 base sequences (and not to the whole reference genome) and extract only the mapped reads. Can I do this with bowtie2, using the ~2700 base sequences as a reference? If so, do you have any advice how to change the default settings so that I can map appropriately?

Thank you so much in advance!

Answer 1

[GenoMax]

You could but if you have data that came from entire genome/larger reference then you can get some spurious mapping (reads mapping even though they may not have originated from the ~2.7K bases). It would be best to map to entire genome and then extract reads that span regions of interest.

[victoriahristovaa]

Thank you so much!

Answer 2

[Lila M]

You can do it but is much better to map to genome of interest and then extract the region you are interested in

[Lila M]

duplicated reply sorry! I haven't seen the other reply when I was writing