RNA-seq data from Illumina/Solexa

[darshan]

I cannot find exact answers to these questions. Please help.

1. If gene A is in +ve strand, will the RNA-seq reads also match the exons from +ve strand of the genome. Will there also be reads whose reverse complement match the -ve strand.

e.g.
chromosome = CACACA CAC ATGT GTGTG
gene = exon1 and exon2
exon1 = position 1 to position 6
exon2 = position 10 to position 13
transcript = CACACAATGT

a. will the illumina RNA-seq reads match (part of ) transcript exactly
read = CACACAATGT
b. Can the illumina RNA-seq reads match th reverse of (part of ) transcript
read = GTGTAACACA
c. Will there be an illumina read complementary to the transcript
read = TGTGTTACAC
d. Will there be an illumina read reverse complementary to the transcript
CACATTGTGT

2. Same question for PER
i. If the first read of the pair is from +ve strand, the second read of the pair has be from the -ve strand; and it has to be reverse.
ii. Does the strand of first read also tells that gene is also from the same strand.

Thanks
Darshan

[krobison]

Look carefully at how the RNA-Seq library is prepared -- some protocols are not strand-specific.

Also, even directional libraries seem to have a certain level of "wrong" strand transcripts, resulting either from antisense transcription in the genome or a certain level of second strand DNA synthesis in the original RT reaction

[asr]

antisense in C. elegans

There is a thread on the WormBase forum about antisense transcription with several examples derived from RNAseq data.

http://www.wormbase.org/forums/index.php?topic=740.0

[steven]

An alternative to antisense transcription for explaining antisense transcripts: http://seqanswers.com/forums/showthread.php?t=6365