Issues with gene id after using Cufflinks

[nmfly]

Hi,

I am very new and very much a beginner when it come to NGS technologies. I have aligned my RNAseq reads to the dm3 genome in galaxy (UCSC dm3 Drosophila annotation). For some reason the gene_ids are all annotated as CUFF.6 or CUFF.1 etc. but I would hope and expect gene-id to be CG numbers from the annotation...

Would anyone know what I have done wrong?

Thanks in advance for any insight

[Krish_143]

I do not know about galaxy, but if you use tophat with -G option (Annotation file)and cufflinks ( annotation file) you will get output with scaffold names.. else it would be like this CUFF.XXXXX.
It's not a problem your doing correct, those are Cufflinks transcripts.

[nmfly]

Sorry I still don't understand

I am using UCSC drosophila genome annotation when performing cufflinks so shouldn't the annotation come from the UCSC file and therefore display gene_id from USCS annotation?

If I can't change the output from CUFF.XXXX, does anyone know how I can identify the gene easily with the CUFF.XXXX gene_ID?

[Krish_143]

if you want to identify gene names for Cuff.XXX
i.e 2 ways :

1) you have to run tophat for mapping instead of galaxy and use -G option in tophat and provide ur UCSC annotation file and run cufflinks for tophat data.

2) perform Blast2go for Cuff.xxxx transcripts here you will identify gene names.

i hope you will understand !

[nmfly]

Hi Krishna,

Thank you, now I understand

I recieved BAM and BED files from another institute which were from tophat. I am not sure what reference genome they used, so maybe that is my issue!

I will contact them and in the meantime give Blast2go a go.

[Krish_143]

Thats fine.. you can ask exactly what genome and annotation file they used.. that has to be fixed through out the project so be clear with that.
tc good luck with blast2go.

[cufflinksman]

Cufflinks

Thats excellent.. you can ask exactly what genome and annotation computer file they used.. that has to be set through out the venture so be obvious with that.
tc best of fortune with blast2go.