I have a 150bp short read whole-genome library by analyzing which I am trying to discover the breakpoint of a possible insertional mutation in a plant genome.
I am wondering Is there any read-mapping package that could map only the first half (e.g. 75bp) or the second half of reads?
Thank you very much.
Hi,
You could use established tools for this purpose. Try a full length mapping of the reads against your reference genome sequence. REAPR (Article REAPR: A universal tool for genome assembly evaluation
), DISCOVAR (https://software.broadinstitute.org/software/discovar/blog/), or variant detection via CLC GenomicsWorkbench would be some examples to identify differences between the reference sequence and the origin of your sequencing reads. However, there is a number of other tools available for this task. It might be useful to compare some results.If you are looking for an insertion, it might be easier to analyze the read coverage depth of your mapping. samtools or featureCounts enable the quantification of reads at a specific position of your mapping. However, this is more complicated if the insertion is not completely new in the genome. Finding copy number variations based on coverage differences requires a high read coverage to compensate for random fluctuations.
Good luck!
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