Query on bowtie2

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3.9 years ago

Domu • 0

Instead of a complete reference genome, I have contigs of the reference to which I want to align my Illumina reads. Can bowtie2 be used for this purpose? I am not sure how it deals with reads which fall at the contig breakpoints, does it still align them?

Thanks!

alignment genome • 643 views

ADD COMMENT • link 3.9 years ago by Domu • 0

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You can use any sequence as reference including contigs when you create bowtie2 indexes. If a read aligns to two contigs you should be able to see if it is aligning at ends of contigs.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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Thanks! So I can check this with IGV?

ADD REPLY • link 3.9 years ago by Domu • 0

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In theory. You may need to find alignments that explicitly have alignments to two contigs and see what those look like in IGV. Here is an overview paper for variant review using IGV.

ADD REPLY • link 3.9 years ago by GenoMax 141k

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Thanks a lot! This really helps

ADD REPLY • link 3.9 years ago by Domu • 0

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