Question: Hi,

I am interested in building an updated annotation of the mouse olfactory receptor genes. They have a tissue specific expression obviously, with various 3' isoforms, so the current annotation is not very good. Hand annotation using IGV to visualize my data is not an option with this gene family ;)

I have mapped RNA Seq paired ends reads from olfactory epithelia to the mm10 genome with STAR, and then I used a new tool called [IsoSCM][1] to obtain a more precise annotation (as a GTF file). It is a de novo approach.

My problem is that I can't easily (it seems) merge this new annotation with the 'official' one (mm10.gtf), which has less precise 5' and 3' (as seen in IGV) but includes Ensembl Gene IDs which I would very much like to have. I am including examples below of both syntaxes.

I would like to know if there is a tool that allows to add the Ensembl Gene IDs to a de novo transcriptome according to the features' position in the genome. I think someone already had to answer this type of question....

Otherwise, I can code simple stuff such as sorting features by their position in the genome and finding reasonable rules for merging (a feature from the new genome which has the same start or end position in mm10.gtf could inherit the mm10.gtf gene ID). Determining the feature type (5', CDS, exon, 3') is a bit more complex but possible.

Here is the mm10.gtf annotation:

```
[cyril@synapse ~]$ head -20 mm10.gtf
chr1 mm10_ensGene stop_codon 134202951 134202953 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
chr1 mm10_ensGene CDS 134202954 134203590 0.000000 - 1 gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
chr1 mm10_ensGene exon 134199223 134203590 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
chr1 mm10_ensGene CDS 134234015 134234355 0.000000 - 0 gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
chr1 mm10_ensGene start_codon 134234353 134234355 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
chr1 mm10_ensGene exon 134234015 134234412 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
chr1 mm10_ensGene exon 134235228 134235431 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465";
```

And the one I obtain with IsoSCM:

```
[cyril@synapse ~]$ head -20 isoSCM.gtf
chr4_JH584293_random sol exon 10822 11047 0.0 + . locus_id "locus.00000000";type "5p_exon"
chr4_JH584293_random sol exon 11191 11251 0.0 + . locus_id "locus.00000000";type "internal_exon"
chr4_JH584293_random sol exon 12077 12246 0.0 + . locus_id "locus.00000000";type "internal_exon"
chr4_JH584293_random sol exon 12375 12489 0.0 + . locus_id "locus.00000000";type "internal_exon"
chr4_JH584293_random sol exon 12643 12675 0.0 + . locus_id "locus.00000000";type "internal_exon"
chr4_JH584293_random sol exon 12754 12920 0.0 + . locus_id "locus.00000000";type "internal_exon"
chr4_JH584293_random sol exon 13477 13640 0.0 + . locus_id "locus.00000000";type "internal_exon"
chr4_JH584293_random sol exon 14817 14989 0.0 + . locus_id "locus.00000000";type "3p_exon"
chr4_JH584293_random sol exon 15884 15933 0.0 + . locus_id "locus.00000001";type "5p_exon"
```

Thanks for your help!

[1]: https://github.com/shenkers/isoscm

Answer: Use [cuffcompare][1] to compare your de novo gtf with mm10 gtf. Then look for [class code][2] j, which I think stands for novel isoform. You can play around.

[1]: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/
[2]: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/