Question: What does a 'normal' FASTQC report look like for scRNA-seq data?
6 weeks ago by
MutationalMeltdown • 20
MutationalMeltdown • 20 wrote:
I'm interested specifically in 'failures' I got on R2 (R1 being just the barcode + UMI). Note this is 10X sincle cell RNA-sequencing (scRNA-seq) data.
- Per tile sequence quality (quality appears slightly worse at about 54bp (the middle of the read), with a corresponding increase in Ns; I'm not sure how to interpret this, having read this)
- Per base sequence content (at start of read only, for this reason I think)
- Per sequence GC content (there is a shifted peak to the left, i.e. AT-rich)
- Sequence Duplication Levels (I guess due to highly expressed genes)
- Overrepresented sequences (no hits; up to 1%)
- Kmer Content (again at start of read only)
Thank you for your help in interpreting this!
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