Hello,
I am using IsoEM to estimate isoform expression level.
As input, I provide a SAM file and a gtf file :
I did this GTF file from a GFF file :
With the information that I got, I figured out that I must keep only the lines "exon". Am I right? I don't see how IsoEM can know the isoforms if I do like this...
As a result, I get 2 files. The one called ...iso_estimates gives:
I understand that the result is the exon expression level estimation and not the isoform expression level estimation. Do I interpret badly the results?
Has someone use IsoEM to this purpose? Do I have a good input GTF file?
How to get the isoform expression level estimation?
Thanks for your help,
Jane
I am using IsoEM to estimate isoform expression level.
As input, I provide a SAM file and a gtf file :
Code:
DS571145 alternativeSplicer exon 3484 4143 . - . gene_id "EHI_151170"; transcript_id "exon_EHI_151170.ref-1"; DS571145 alternativeSplicer exon 3484 3943 . - . gene_id "EHI_151170"; transcript_id "exon_EHI_151170.alt1-1"; DS571145 alternativeSplicer exon 3997 4143 . - . gene_id "EHI_151170"; transcript_id "exon_EHI_151170.alt1-2"; ...
Code:
DS571145 alternativeSplicer gene 3484 4143 . - . ID=EHI_151170;Name=hypothetical protein; DS571145 alternativeSplicer mRNA 3484 4143 . - . ID=EHI_151170.ref;Name=EHI_151170.ref;Parent=EHI_151170;completeORF=yes DS571145 alternativeSplicer exon 3484 4143 . - . ID=exon_EHI_151170.ref-1;Name=exon;Parent=EHI_151170.ref; DS571145 alternativeSplicer mRNA 3484 4143 . - . ID=EHI_151170.alt1;Name=EHI_151170.alt1;Parent=EHI_151170;completeORF=no DS571145 alternativeSplicer exon 3484 3943 . - . ID=exon_EHI_151170.alt1-1;Name=exon;Parent=EHI_151170.alt1; DS571145 alternativeSplicer exon 3997 4143 . - . ID=exon_EHI_151170.alt1-2;Name=exon;Parent=EHI_151170.alt1; ...
As a result, I get 2 files. The one called ...iso_estimates gives:
Code:
... exon_EHI_151170.ref-1 37.03955548991607 ... exon_EHI_151170.alt1-1 0.0 exon_EHI_151170.alt1-2 0.0 ...
Has someone use IsoEM to this purpose? Do I have a good input GTF file?
How to get the isoform expression level estimation?
Thanks for your help,
Jane
Comment