Question: how bowtie deals with reads cowering simultaneously 5` and 3` ends of DNA fragment
gravatar for k.panov
2.7 years ago by
k.panov0 wrote:

Hello, I need to add an extra genomic DNA to a genome assembly. 40% of this DNA encodes transcript, 60% isn’t transcribed but contains various regulatory elements as well as big region of non-coding sequence without any known functions. Historically, numeration (and importantly annotation) of this DNA begins from +1 of transcript and as result promoter is located at the 3-prime end. This is circular DNA, so in vivo +1 site follows the promoter. However, it will be added as linear fragment and I wonder what will happened when bowtie will attempt to align reads which begin at the promoter region and span into the transcribed part? Will it still align part of a read to 5-prime end and another part to 3-prime end of this DNA and give low scoring, or it will discard a read entirely?

ADD COMMENTlink modified 2.7 years ago by Devon Ryan97k • written 2.7 years ago by k.panov0
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

If you use --local (assuming bowtie2 rather than bowtie 1) then you'll get partial alignments at one of the ends. Note that you will still see a decrease in coverage near the ends and you won't have reads with portions mapping to both ends of the contig. This is a case where bwa mem might be preferable, since it also produces supplementary alignments (so it can align part to each end of the contig).

ADD COMMENTlink written 2.7 years ago by Devon Ryan97k
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