Possibility of mapping opposite strand

Question

[dahun73]

Hello All,

I have question about RNA-seq data(exactly speaking, it is eCLIP-seq). For different library types, I heard FASTQ sequence is complementary with original RNAs. If so, is there any possibility of mapping opposite strand? I made a bigwig file to watch in UCSC genome browser. But some of genes seem to be expressed opposite strand. How can I figure out whether FASTQ sequences is the same of original RNAs or not?

Answer 1

[swbarnes2]

Genes run forward and backwards, so of course even a stranded protocol will run both forward and backwards when compared to the genome.

Ask Illumina which way the strandedness goes, or look yourself at how the reads align compared to the direction of individual transcripts.