Question: Query on bowtie2
0
gravatar for Domu
7 months ago by
Domu0
Domu0 wrote:

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 • 184 views
ADD COMMENTlink written 7 months ago by Domu0

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 REPLYlink modified 7 months ago • written 7 months ago by GenoMax95k

Thanks! So I can check this with IGV?

ADD REPLYlink written 7 months ago by Domu0

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 REPLYlink written 7 months ago by GenoMax95k

Thanks a lot! This really helps

ADD REPLYlink written 7 months ago by Domu0
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