Dear all,
I am doing 2x100 paired-end (PE) exome sequencing on an Illumina machine with the Nextera rapid capture exome capture protocol. Since over 80% of the target Nextera target exons are shorter then 200bp, I get many overlapping PE reads.
I now wonder if doing 2x100 bp is a good approach in this case. I realize that it depends on how you treat the overlapping PE reads. I invite you to contribute to this discussion here:
http://seqanswers.com/forums/showthread.php?t=61369
An obvious solution might be to do shorter reads, i.e. 2x50 bp, however the kit to do 100bp (2x50) cost almost as much as the kit to do 200bp (2x100), so there is little gain.
Might it actually be better to do SE sequencing here to avoid overlapping, to avoid sequencing the same DNA fragment twice? Disadvantages of SE sequencing are less accurate duplicate recognition, though this problem occurs just with very high coverage and my coverage is rather moderate (40-60X). The advantage is that I will have more independent reads, i.e. more data.
I'd appreciate your thoughts. Thank you.
I am doing 2x100 paired-end (PE) exome sequencing on an Illumina machine with the Nextera rapid capture exome capture protocol. Since over 80% of the target Nextera target exons are shorter then 200bp, I get many overlapping PE reads.
I now wonder if doing 2x100 bp is a good approach in this case. I realize that it depends on how you treat the overlapping PE reads. I invite you to contribute to this discussion here:
http://seqanswers.com/forums/showthread.php?t=61369
An obvious solution might be to do shorter reads, i.e. 2x50 bp, however the kit to do 100bp (2x50) cost almost as much as the kit to do 200bp (2x100), so there is little gain.
Might it actually be better to do SE sequencing here to avoid overlapping, to avoid sequencing the same DNA fragment twice? Disadvantages of SE sequencing are less accurate duplicate recognition, though this problem occurs just with very high coverage and my coverage is rather moderate (40-60X). The advantage is that I will have more independent reads, i.e. more data.
I'd appreciate your thoughts. Thank you.
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