Hello everyone,
I'm analyzing an RNA-Seq experiment and I'm looking for some advice about how to interpret an anomaly that I'm seeing.
I opened up the alignments for each of my samples in IGV, because I wanted to look at the alignment for the Rbpj gene, a gene that I'm interested in, but for which I didn't get quite high enough coverage to analyze.
I noticed I had a number of reads hit the same location between exons 1 and 2 in all of my samples, but that that region was not annotated as an exon (see attached screen shot).
I checked out the annotations for the gene on ...
UCSC: http://genome.ucsc.edu/cgi-bin/hgTra...ches=NM_009035,
... and Ensembl: http://useast.ensembl.org/Mus_muscul...55779-53657445
In both cases, it appears that there is an exon (or something) between the first and second exons of Rbjp (right where my reads are hitting) in some entries, but not in others.
I'm looking for some help in figuring out what to make of this. Is this a real exon that didn't make it into the mm9 annotation?
Thanks,
Alex
Some additional Info:
I'm analyzing an RNA-Seq experiment and I'm looking for some advice about how to interpret an anomaly that I'm seeing.
I opened up the alignments for each of my samples in IGV, because I wanted to look at the alignment for the Rbpj gene, a gene that I'm interested in, but for which I didn't get quite high enough coverage to analyze.
I noticed I had a number of reads hit the same location between exons 1 and 2 in all of my samples, but that that region was not annotated as an exon (see attached screen shot).
I checked out the annotations for the gene on ...
UCSC: http://genome.ucsc.edu/cgi-bin/hgTra...ches=NM_009035,
... and Ensembl: http://useast.ensembl.org/Mus_muscul...55779-53657445
In both cases, it appears that there is an exon (or something) between the first and second exons of Rbjp (right where my reads are hitting) in some entries, but not in others.
I'm looking for some help in figuring out what to make of this. Is this a real exon that didn't make it into the mm9 annotation?
Thanks,
Alex
Some additional Info:
- Illumina paired-end reads
- Aligned reads to mm9 with STAR 2.3.0
- I used HTSeq-count to count the reads mapping to genes. The counts were very low for Rbpj (too low for differential expression analysis), but they could have been quite a bit higher if this phantom exon had been included in the annotation.
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