Thank you so much!
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victoriahristovaa •
Mapping reads to a very small reference
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!
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Lila M
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victoriahristovaa •
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victoriahristovaa •
2 answers
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.
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