Hi,
I apologize if this has been covered but I can't find an answer for the issue that I am seeing with some paired-end Chip-seq data.
In all of my samples the second read shows poor quality scores after ~15 nt, and it appears that those first 15 nt are a stretch of poly-a (as determined by FastQC). These were not trimmed, I just wanted to assess the quality of the reads up front. The first read of the pair looks good.
Any thoughts what could be causing this? Is this an issue with library prep?
Thanks
I apologize if this has been covered but I can't find an answer for the issue that I am seeing with some paired-end Chip-seq data.
In all of my samples the second read shows poor quality scores after ~15 nt, and it appears that those first 15 nt are a stretch of poly-a (as determined by FastQC). These were not trimmed, I just wanted to assess the quality of the reads up front. The first read of the pair looks good.
Any thoughts what could be causing this? Is this an issue with library prep?
Thanks
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