mRNA Seq

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20 months 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.

NGS • 788 views

ADD COMMENT • link updated 20 months ago by Ram 44k • written 20 months ago by Yaseen ▴ 10

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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.

ADD REPLY • link 20 months ago by iraun 6.2k

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Is this classic/old-school/ ... bulk RNAseq you did?

so not any other flavour, such as single cell, amplicon, ... ?

ADD REPLY • link 20 months ago by lieven.sterck 15k

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I have done mRNA sequencing...

As lieven.sterck asks: what was the RNA purification method? What was the library construction method? What was the sequencing technology?

ADD REPLY • link 20 months ago by seidel 11k

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