Question: RNAseq exon count
gravatar for veerle
6 weeks ago by
veerle0 wrote:

Hej, I have an RNAseq dataset (single end) from a mouse model heterozygous for a trapped-gene. The construct is located between exon 1 and 2 of our target gene and any transcripts derived from this allele should be spliced from exon 1 to the construct, which contains a polyA signal to terminate transcription. When comparing the expression levels to wildtypes, no overal difference in expression of the target gene is found. We believe it might be due to exon 1 being present in both wildtype allele and knockout allele.

We wish to count exon reads (for exon 2-12) for our gene of interest, and compare the expression levels of between genotypes. Anyone can help me? What tool to use, which settings?

Thank you,

exon rna-seq • 73 views
ADD COMMENTlink modified 5 weeks ago by Jennifer Hillman Jackson25k • written 6 weeks ago by veerle0
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


You'll need to perform differential expression analysis at the transcript level (not gene).

Please see the Galaxy tutorials here for example workflows:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 weeks ago by Jennifer Hillman Jackson25k
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