This is first time I used your cufflink software. I don't understand some of warning messager from the cuffcompare command line. I am using the lastest version cufflinks-0.8.2.Linux_x86_64.
I download the reference annotation GTF files (human ensembl and refseq ) from UCSC table browser.
1) UCSC human ensembl GTF file:
chr1 hg19_ensGene CDS 67126196 67126207 0.000000 + 0 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene exon 67126196 67126207 0.000000 + . gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene CDS 67133213 67133224 0.000000 + 0 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene exon 67133213 67133224 0.000000 + . gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene CDS 67136678 67136702 0.000000 + 0 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene exon 67136678 67136702 0.000000 + . gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene CDS 67137627 67137678 0.000000 + 2 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
2) cuffcompare command line:
/usca/clscratch/geru1/cufflinks-0.8.2.Linux_x86_64/cuffcompare -r /usca/home/geru1/gtf/refgene.gtf -o s_1_and_s_2.txt -R -s /usca/clscratch/geru1/bowtie-0.12.5/indexes/ ./testme/transcripts.gtf ./testme_s2/transcripts.gtf
3) Warning messager from cuffcompare:
GFF Warning: discarded overlapping feature segment (3019321-3021003) for GFF ID ENST00000416194
GFF Warning: discarded overlapping feature segment (2990575-2990576) for GFF ID ENST00000439917
GFF Warning: discarded overlapping feature segment (2904529-2904530) for GFF ID ENST00000431516
GFF Warning: discarded overlapping feature segment (2933284-2934966) for GFF ID ENST00000383431
GFF Warning: discarded overlapping feature segment (2953771-2953772) for GFF ID ENST00000436814
GFF Warning: discarded overlapping feature segment (2982531-2984213) for GFF ID ENST00000457089
GFF Warning: discarded overlapping feature segment (2941694-2941695) for GFF ID ENST00000423612
GFF Warning: discarded overlapping feature segment (2970446-2972128) for GFF ID ENST00000437010
Warning: transcript ENST00000370343 discarded (structural errors found, length=88047).
Warning: transcript ENST00000401006 discarded (structural errors found, length=22054).
Warning: transcript ENST00000465119 discarded (structural errors found, length=35491).
Warning: transcript ENST00000448632 discarded (structural errors found, length=26138).
Warning: transcript ENST00000444385 discarded (structural errors found, length=41396).
Warning: transcript ENST00000447431 discarded (structural errors found, length=30178).
Warning: transcript ENST00000372433 discarded (structural errors found, length=2407).
Thank you in advances!
Robin
I download the reference annotation GTF files (human ensembl and refseq ) from UCSC table browser.
1) UCSC human ensembl GTF file:
chr1 hg19_ensGene CDS 67126196 67126207 0.000000 + 0 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene exon 67126196 67126207 0.000000 + . gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene CDS 67133213 67133224 0.000000 + 0 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene exon 67133213 67133224 0.000000 + . gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene CDS 67136678 67136702 0.000000 + 0 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene exon 67136678 67136702 0.000000 + . gene_id "ENST00000237247"; transcript_id "ENST00000237247";
chr1 hg19_ensGene CDS 67137627 67137678 0.000000 + 2 gene_id "ENST00000237247"; transcript_id "ENST00000237247";
2) cuffcompare command line:
/usca/clscratch/geru1/cufflinks-0.8.2.Linux_x86_64/cuffcompare -r /usca/home/geru1/gtf/refgene.gtf -o s_1_and_s_2.txt -R -s /usca/clscratch/geru1/bowtie-0.12.5/indexes/ ./testme/transcripts.gtf ./testme_s2/transcripts.gtf
3) Warning messager from cuffcompare:
GFF Warning: discarded overlapping feature segment (3019321-3021003) for GFF ID ENST00000416194
GFF Warning: discarded overlapping feature segment (2990575-2990576) for GFF ID ENST00000439917
GFF Warning: discarded overlapping feature segment (2904529-2904530) for GFF ID ENST00000431516
GFF Warning: discarded overlapping feature segment (2933284-2934966) for GFF ID ENST00000383431
GFF Warning: discarded overlapping feature segment (2953771-2953772) for GFF ID ENST00000436814
GFF Warning: discarded overlapping feature segment (2982531-2984213) for GFF ID ENST00000457089
GFF Warning: discarded overlapping feature segment (2941694-2941695) for GFF ID ENST00000423612
GFF Warning: discarded overlapping feature segment (2970446-2972128) for GFF ID ENST00000437010
Warning: transcript ENST00000370343 discarded (structural errors found, length=88047).
Warning: transcript ENST00000401006 discarded (structural errors found, length=22054).
Warning: transcript ENST00000465119 discarded (structural errors found, length=35491).
Warning: transcript ENST00000448632 discarded (structural errors found, length=26138).
Warning: transcript ENST00000444385 discarded (structural errors found, length=41396).
Warning: transcript ENST00000447431 discarded (structural errors found, length=30178).
Warning: transcript ENST00000372433 discarded (structural errors found, length=2407).
Thank you in advances!
Robin
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