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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
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error:discarding overlapping duplicate gene feature during assembly process #355

Closed ravisaroch closed 2 years ago

ravisaroch commented 2 years ago

Hi,

I am getting this error while trying to assemble the individual sample using stringtie v2.1.4. How do I resolve it?

stringtie error Error: discarding overlapping duplicate gene feature (20524022-20525760) with ID=gene:BGIOSGA029322 Error: discarding overlapping duplicate mRNA feature (20524022-20525760) with ID=transcript:BGIOSGA029322-TA Error: discarding overlapping duplicate ncRNA_gene feature (20526553-20526635) with ID=gene:ENSRNA049494864 Error: discarding overlapping duplicate pre_miRNA feature (20526553-20526635) with ID=transcript:ENSRNA049494864-T1 Error: discarding overlapping duplicate gene feature (20550358-20552171) with ID=gene:BGIOSGA029321 Error: discarding overlapping duplicate mRNA feature (20550358-20552171) with ID=transcript:BGIOSGA029321-TA Error: discarding overlapping duplicate gene feature (20555133-20556645) with ID=gene:BGIOSGA031218 . . . . . Error: discarding overlapping duplicate mRNA feature (20555133-20556645) with ID=transcript:BGIOSGA031218-TA Error: discarding overlapping duplicate gene feature (20560901-20565807) with ID=gene:BGIOSGA031219 Error: discarding overlapping duplicate mRNA feature (20560901-20565807) with ID=transcript:BGIOSGA031219-TA Error: discarding overlapping duplicate gene feature (20568769-20569820) with ID=gene:BGIOSGA029320 Error: discarding overlapping duplicate mRNA feature (20568769-20569820) with ID=transcript:BGIOSGA029320-TA Error: discarding overlapping duplicate gene feature (20570747-20571860) with ID=gene:BGIOSGA031220 Error: discarding overlapping duplicate mRNA feature (20570747-20571860) with ID=transcript:BGIOSGA031220-TA

Command stringtie -p 30 -G myfile.gff3 -o AK10_S10_L001.gtf AK10_S10_L001.bam -l AK10_S10_L001

Example gff3 file 1 bgi gene 470346 473434 . - . ID=gene:BGIOSGA002547;biotype=protein_coding;gene_id=BGIOSGA002547;logic_name=genemodel_riceindica_bgi 1 bgi mRNA 470346 473434 . - . ID=transcript:BGIOSGA002547-TA;Parent=gene:BGIOSGA002547;biotype=protein_coding;transcript_id=BGIOSGA002547-TA 1 bgi exon 470346 470747 . - . Parent=transcript:BGIOSGA002547-TA;Name=BGIOSGA002547-TA.9;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=BGIOSGA002547-TA.9;rank=9 1 bgi CDS 470346 470747 . - 0 ID=CDS:BGIOSGA002547-PA;Parent=transcript:BGIOSGA002547-TA;protein_id=BGIOSGA002547-PA 1 bgi exon 470833 470903 . - . Parent=transcript:BGIOSGA002547-TA;Name=BGIOSGA002547-TA.8;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=BGIOSGA002547-TA.8;rank=8 1 bgi CDS 470833 470903 . - 2 ID=CDS:BGIOSGA002547-PA;Parent=transcript:BGIOSGA002547-TA;protein_id=BGIOSGA002547-PA 1 bgi exon 471015 471060 . - . Parent=transcript:BGIOSGA002547-TA;Name=BGIOSGA002547-TA.7;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=BGIOSGA002547-TA.7;rank=7 1 bgi CDS 471015 471060 . - 0 ID=CDS:BGIOSGA002547-PA;Parent=transcript:BGIOSGA002547-TA;protein_id=BGIOSGA002547-PA 1 bgi exon 471187 471218 . - . Parent=transcript:BGIOSGA002547-TA;Name=BGIOSGA002547-TA.6;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=BGIOSGA002547-TA.6;rank=6 1 bgi CDS 471187 471218 . - 2 ID=CDS:BGIOSGA002547-PA;Parent=transcript:BGIOSGA002547-TA;protein_id=BGIOSGA002547-PA 1 bgi exon 471552 471735 . - . Parent=transcript:BGIOSGA002547-TA;Name=BGIOSGA002547-TA.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=BGIOSGA002547-TA.5;rank=5 1 bgi CDS 471552 471735 . - 0 ID=CDS:BGIOSGA002547-PA;Parent=transcript:BGIOSGA002547-TA;protein_id=BGIOSGA002547-PA 1 bgi exon 471820 471995 . - . Parent=transcript:BGIOSGA002547-TA;Name=BGIOSGA002547-TA.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=BGIOSGA002547-TA.4;rank=4 1 bgi CDS 471820 471995 . - 2 ID=CDS:BGIOSGA002547-PA;Parent=transcript:BGIOSGA002547-TA;protein_id=BGIOSGA002547-PA