Blondeau-Bidet
commented
7 months ago Update: This time I've re-run the analysis with REFseq type data (fasta and GTF) downloaded from NCBI and used Kallisto for quantification with the fasta file of the transcripts.
aSwitchList_2 <- importRdata( isoformCountMatrix = Kallisto_Quant$counts, isoformRepExpression = Kallisto_Quant$abundance, designMatrix = myDesign, isoformExonAnnoation ="D:/Salsa_Intolerants/IsoformSwitchAnalyseR/Genome_2021_ncbi/Dl_2021_ncbi_annotation.gtf", isoformNtFasta = "D:/Salsa_Intolerants/IsoformSwitchAnalyseR/Genome_2021_ncbi/Dl_2021_rna.fa", fixStringTieAnnotationProblem = TRUE, removeNonConvensionalChr = TRUE, ignoreAfterBar = TRUE, ignoreAfterSpace = TRUE, ignoreAfterPeriod = TRUE, showProgress = FALSE )
And I get the same error message. I don't understand the source of the problem.
Erreur dans importRdata(isoformCountMatrix = Kallisto_Quant$counts, isoformRepExpression = Kallisto_Quant$abundance, : The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (Jaccard similarity < 0.925). Either isforoms found in the annotation are not quantifed or vise versa. Specifically: 0 isoforms were quantified. 64646 isoforms are annotated. Only 0 overlap. 0 isoforms quantifed had no corresponding annoation
This combination cannot be analyzed since it will cause discrepencies between quantification and annotation thereby skewing all analysis.
If there is no overlap (as in zero or close) there are two options:
1) The files do not fit together (e.g. different databases, versions, etc) (no fix except using propperly paired files).
2) It is somthing to do with how the isoform ids are stored in the different files. This problem might be solvable using some of the 'ignoreAfterBar', 'ignoreAfterSpace' or 'ignoreAfterPeriod' arguments.
Examples from expression matrix are :
Examples of annoation are : XM_051383982, XM_051399489, XM_051407153
Examples of isoforms which were only found im the quantification are :
chunxubioinfor
Hello, I am encountering an error when importing data into R. I used STAR + RSEM to quantify my data. A genome and an annotation file are available on Ensembl. I don't understand the error because I can find the same genes and isoforms in my counting matrix and in my annotation file. I've checked several times and the fasta and gtf files used for mapping + quantification are indeed the same as those indicated in the command line under R. Attached is a file with a preview of a count matrix for 1 sample, followed by my annotation file. Overview_counts_annotation.txt
Thank you for your help,
Eva
Here is my command line :
aSwitchList_2 <- importRdata( isoformCountMatrix = RSEM_Quant$counts, isoformRepExpression = RSEM_Quant$abundance, designMatrix = myDesign, isoformExonAnnoation = "Dicentrarchus_labrax.dlabrax2021.111.gtf", isoformNtFasta = "Dicentrarchus_labrax.dlabrax2021.dna.toplevel.fa", fixStringTieAnnotationProblem = FALSE, removeNonConvensionalChr = TRUE, ignoreAfterBar = TRUE, ignoreAfterSpace = TRUE, ignoreAfterPeriod = TRUE, showProgress = FALSE )And here is the error message:
_Erreur dans importRdata(isoformCountMatrix = RSEM_Quant$counts, isoformRepExpression = RSEM_Quant$abundance, : The annotation and quantification (count/abundance matrix and isoform annotation) seems to be different (Jaccard similarity < 0.925). Either isforoms found in the annotation are not quantifed or vise versa. Specifically: 0 isoforms were quantified. 69565 isoforms are annotated. Only 0 overlap. 0 isoforms quantifed had no corresponding annoation
This combination cannot be analyzed since it will cause discrepencies between quantification and annotation thereby skewing all analysis.
If there is no overlap (as in zero or close) there are two options: 1) The files do not fit together (e.g. different databases, versions, etc) (no fix except using propperly paired files). 2) It is somthing to do with how the isoform ids are stored in the different files. This problem might be solvable using some of the 'ignoreAfterBar', 'ignoreAfterSpace' or 'ignoreAfterPeriod' arguments. Examples from expression matrix are :
Examples of annoation are : ENSDLAT00005029896, ENSDLAT00005056072, ENSDLAT00005077077 Examples of isoforms which were only found im the quantification are :_