Hi all,
I’ve been working on an RNA-Seq project and have encountered a significant issue with my data quality after library preparation. Initially, our sequencing runs had expected read quality, but after performing library prep, the reads dropped in quality, with many reads showing lower Phred scores than expected. This drop is impacting the alignment and downstream analysis, and I’m trying to understand what could be causing it.
Has anyone else experienced this issue after library prep, and if so, what steps did you take to resolve it? Are there specific aspects of the library preparation process that could contribute to this, such as adapter contamination or incomplete fragmentation?
Additionally, I’ve noticed some low-quality bases around the read ends. Would trimming or filtering these poor-quality bases improve the data quality for downstream analysis like differential expression analysis?
Any advice or insights would be greatly appreciated!
Thanks in advance for your help,
Alicent Hightower Block Blast
I’ve been working on an RNA-Seq project and have encountered a significant issue with my data quality after library preparation. Initially, our sequencing runs had expected read quality, but after performing library prep, the reads dropped in quality, with many reads showing lower Phred scores than expected. This drop is impacting the alignment and downstream analysis, and I’m trying to understand what could be causing it.
Has anyone else experienced this issue after library prep, and if so, what steps did you take to resolve it? Are there specific aspects of the library preparation process that could contribute to this, such as adapter contamination or incomplete fragmentation?
Additionally, I’ve noticed some low-quality bases around the read ends. Would trimming or filtering these poor-quality bases improve the data quality for downstream analysis like differential expression analysis?
Any advice or insights would be greatly appreciated!
Thanks in advance for your help,
Alicent Hightower Block Blast