Hi,
we are starting to analyze a PE 100 run of a resequencing project. Unfortunately the library is too short and the majority of paired-end reads overlap. In this study we are interested in SNPs, INDELs and big rearrangements.
What could be the best option? Cut the 100 bp fragments and leave them in 75 bp (for example) or using the 100 bp overlapping reads? Do the advantages of the PE get lost if the reads are overlapped?
Thanks in advance for your help.
we are starting to analyze a PE 100 run of a resequencing project. Unfortunately the library is too short and the majority of paired-end reads overlap. In this study we are interested in SNPs, INDELs and big rearrangements.
What could be the best option? Cut the 100 bp fragments and leave them in 75 bp (for example) or using the 100 bp overlapping reads? Do the advantages of the PE get lost if the reads are overlapped?
Thanks in advance for your help.
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