The correct RNA-seq Reference genome
I'm doing RNA-seq and used the seqkit tool to count the number of reads in the Fastq file. The tool indicates that my data is of the DNA kind. I am unsure of the type's reliability here.
I am using this files:
Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
Is the reference genome the cause of this? Is it possible that I'm using the incorrect one because it's titled with dna?
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biofalconch
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وفاء •
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What command did you actually use? Remember that RNA-seq reads are created by first synthesising cDNA out of mRNA molecules, so it makes sense to not have U instead of T's, so yes the reads are fine.