Entering edit mode
9 days ago
Yaseen ▴ 10
I have done mRNA sequencing and I got fastq data, but only Read 1 are aligning to reference genome and R2 is not aligning. Its not proper R1 and R2 alignment. But library qc is fine.
Please let me know about read alignments and why is that not aligning.
Could you provide the commands used for the alignment and some QC stats regarding the data? Otherwise, it is difficult to assess what is going on.
Is this classic/old-school/ ... bulk RNAseq you did?
so not any other flavour, such as single cell, amplicon, ... ?
As lieven.sterck asks: what was the RNA purification method? What was the library construction method? What was the sequencing technology?