Possibility of mapping opposite strand
1
0
Entering edit mode
9 months ago
dahun73 ▴ 10

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?

RNA-Seq STAR FASTQ alignment • 253 views
ADD COMMENT
1
Entering edit mode
9 months ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1601 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6