Hey all,
I've heard that with the new, longer Illumina reads (>100bp), for mate-pair sequencing the amount of chimeric reads has increased strikingly. (Because it is much more likely to read over the junction). Is this true? Anyone having experience from this?
I've searched for information, but the only thing I found was a quite old post saying that Illumina doesn't recommend longer read length than 36bp for mate-pair sequencing.
We are about to sequence one full flowcell of Illumina mate-pairs, and the default read length is now 109bp - will this work or is it better to choose a shorter read length, like 36 or 50bp?
Any advice would be appreciated!
I've heard that with the new, longer Illumina reads (>100bp), for mate-pair sequencing the amount of chimeric reads has increased strikingly. (Because it is much more likely to read over the junction). Is this true? Anyone having experience from this?
I've searched for information, but the only thing I found was a quite old post saying that Illumina doesn't recommend longer read length than 36bp for mate-pair sequencing.
We are about to sequence one full flowcell of Illumina mate-pairs, and the default read length is now 109bp - will this work or is it better to choose a shorter read length, like 36 or 50bp?
Any advice would be appreciated!
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