Hi,
I am testing SplicingCompass for splicing differential expression analysis. Here is the steps:
1. map the rnaseq reads to genome sequence using tophat
2. prepare the gtf file produced by exseq_prepare_annotation.py of DEXSeq package.
3. calculate the counts using coverageBed
Then do the same R scripts as the SplicingCompasstutorial suggest, the
checkExperimentInfo(expInf) command return TRUE, which suggest the "providing experimental information" step is correct.
When I run the command and got the error message:
What's wrong here?
I guess it may be caused by the unprobable gtf annotation file.
I paste several lines of them:
I am testing SplicingCompass for splicing differential expression analysis. Here is the steps:
1. map the rnaseq reads to genome sequence using tophat
2. prepare the gtf file produced by exseq_prepare_annotation.py of DEXSeq package.
3. calculate the counts using coverageBed
Then do the same R scripts as the SplicingCompasstutorial suggest, the
checkExperimentInfo(expInf) command return TRUE, which suggest the "providing experimental information" step is correct.
When I run the command and got the error message:
Code:
> countTable=constructCountTable(countTable,nCores=12,printDotPerGene=TRUE) Processing CoverageBed output files: |======================================================================| 100% Adding gene id column for convenience ...done Adding uniqe id column to table for convenience...done Adding exon numbers...done Adding RPKM values for every exon...done Adding row means ...done Adding row meds...done Adding log ratios...done ==================== ...constructing junction dimensions (this will take some time)... ============== Reading reference annotation... Preprocessing reference annotation (this may take a couple of minutes)...done processing G_1 processing G_2 processing S_1 processing S_2 using 12 cores ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Error in addColConnectsKnownConsecutiveExons(gffOfOneGene, junctionsGene) : Junction connects more than two exons? 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|============ | 17%Error in if (nrow(junctionMatrices[[i]]) > 0) junctionMatrices[[i]]$gene_id = geneIDs[i] : argument is of length zero > >
I guess it may be caused by the unprobable gtf annotation file.
I paste several lines of them:
Code:
scaffold10135 dexseq_prepare_annotation.py exonic_part 178842 179264 0.0000 + . mergedTranscriptIDs "TCONS_000 25194"; exonic_part_number "001"; geneSymbol "XLOC_020700" scaffold10138 dexseq_prepare_annotation.py exonic_part 144830 145048 0.0000 + . mergedTranscriptIDs "TCONS_000 25196"; exonic_part_number "001"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 151927 151979 0.0000 + . mergedTranscriptIDs "TCONS_000 25196"; exonic_part_number "002"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 169424 169664 0.0000 + . mergedTranscriptIDs "TCONS_000 25196"; exonic_part_number "003"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 169424 169664 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "003"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 188724 188960 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "004"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 197955 198114 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "005"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 209088 209291 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "006"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 209982 210216 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "007"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 215577 215763 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "008"; geneSymbol "XLOC_020702" scaffold10138 dexseq_prepare_annotation.py exonic_part 217793 217975 0.0000 + . mergedTranscriptIDs "TCONS_00025196"; exonic_part_number "009"; geneSymbol "XLOC_020702" scaffold1014 dexseq_prepare_annotation.py exonic_part 84574 84743 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "001"; geneSymbol "XLOC_020705" scaffold1014 dexseq_prepare_annotation.py exonic_part 101674 101857 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "002"; geneSymbol "XLOC_020705" scaffold1014 dexseq_prepare_annotation.py exonic_part 121745 121897 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "003"; geneSymbol "XLOC_020705" scaffold1014 dexseq_prepare_annotation.py exonic_part 122021 122095 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "004"; geneSymbol "XLOC_020705" scaffold1014 dexseq_prepare_annotation.py exonic_part 137805 138013 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "005"; geneSymbol "XLOC_020705" scaffold1014 dexseq_prepare_annotation.py exonic_part 146499 146673 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "006"; geneSymbol "XLOC_020705" scaffold1014 dexseq_prepare_annotation.py exonic_part 154828 154938 0.0000 - . mergedTranscriptIDs "TCONS_00025199"; exonic_part_number "007"; geneSymbol "XLOC_020705"
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