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Hallo to everybody.
My name is Alessandro and i’m trying to perform an RNA-seq analysis using CLC Genomic Workbench. Unfortunately I found a lot of troubles and I’m desperately looking for somebody that could help me otr just give an opinion. Basically my main problem is that when I perform the RNA-seq analysis I can’t get any expression value. What I’ve done is:
1) I imported the reference sequence in FASTA format (it represents the 8X coverage of Vitis vinifera genome in Chromosomes)
2) Using the tool “Annotate with gff/gft files” I upload the annotations on this reference sequence (they represent Gene, mRNA, CDS, and UTR).
3) I imported the txt files corresponding to the paired ends reads obtained from my Illumina sequencing on CLC
4) I perform an RNA-seq analysis using one of mine paired and sequences (at this point considered as single reads) and my annotated reference genome.
My trouble is that at the end of my analysis I can actually see the reads aligned on each single gene in my ref-seq, but in the table indicating the expression values, RPKM, the number of transcript ext…ext… there is absolutely nothing. All values are 0.00.
I can’t really understand why…Do you have any idea?? ☹
My name is Alessandro and i’m trying to perform an RNA-seq analysis using CLC Genomic Workbench. Unfortunately I found a lot of troubles and I’m desperately looking for somebody that could help me otr just give an opinion. Basically my main problem is that when I perform the RNA-seq analysis I can’t get any expression value. What I’ve done is:
1) I imported the reference sequence in FASTA format (it represents the 8X coverage of Vitis vinifera genome in Chromosomes)
2) Using the tool “Annotate with gff/gft files” I upload the annotations on this reference sequence (they represent Gene, mRNA, CDS, and UTR).
3) I imported the txt files corresponding to the paired ends reads obtained from my Illumina sequencing on CLC
4) I perform an RNA-seq analysis using one of mine paired and sequences (at this point considered as single reads) and my annotated reference genome.
My trouble is that at the end of my analysis I can actually see the reads aligned on each single gene in my ref-seq, but in the table indicating the expression values, RPKM, the number of transcript ext…ext… there is absolutely nothing. All values are 0.00.
I can’t really understand why…Do you have any idea?? ☹