Hi mates!
How is it going? For me not too good!!
I don't know if anybody is confdent with RNA-seq analysis by clc genomic workbench... Actually i'm trying to look at the transcriptome expression of several semples of treated grapevine leaves against untreated using a 36bp paired ends approach with illumina technology. I never used clc before and i'm not a bioinformatic, so i'm sorry if i'm gonna be a bit generic and unprecise.
To allign all my reads against the 8X reference genome the first think i've to do is to upload my genome on clc and to annotate it. The reference genome is a FASTA file, while annotations are in a GFF format. To annotate the reference genome i use the tool "annotate with a GFF/GTF file". It seems to work, as i can see the annotations on the reference genome in the view window. The problem is that when i try to look at the annotation table i can't do it. The only table i can see show me a list of all different chromosomes on my FASTA file. I point out this becouse, when i make the RNA-seq analysis, despite i can see the reads alligning on the annotations, i can't get any expression value for my genes. Ant i can't see any value in all the other column of the RNA-seq analyzed sample table. I guess there is a problem with the GFF file. But i'm really ignorant about that...Is anybody confident with this kind of analysis?? Does anybody have any suggestion?? I've a LOT of data and i can't analyze it...IT'S SO FROUSTRATING!!!!!!!
Cheers!!
Ale
How is it going? For me not too good!!
I don't know if anybody is confdent with RNA-seq analysis by clc genomic workbench... Actually i'm trying to look at the transcriptome expression of several semples of treated grapevine leaves against untreated using a 36bp paired ends approach with illumina technology. I never used clc before and i'm not a bioinformatic, so i'm sorry if i'm gonna be a bit generic and unprecise.
To allign all my reads against the 8X reference genome the first think i've to do is to upload my genome on clc and to annotate it. The reference genome is a FASTA file, while annotations are in a GFF format. To annotate the reference genome i use the tool "annotate with a GFF/GTF file". It seems to work, as i can see the annotations on the reference genome in the view window. The problem is that when i try to look at the annotation table i can't do it. The only table i can see show me a list of all different chromosomes on my FASTA file. I point out this becouse, when i make the RNA-seq analysis, despite i can see the reads alligning on the annotations, i can't get any expression value for my genes. Ant i can't see any value in all the other column of the RNA-seq analyzed sample table. I guess there is a problem with the GFF file. But i'm really ignorant about that...Is anybody confident with this kind of analysis?? Does anybody have any suggestion?? I've a LOT of data and i can't analyze it...IT'S SO FROUSTRATING!!!!!!!
Cheers!!
Ale
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