gffcompare

Question

[linjc.xmu]

Hi all, I am a new user of StringTie and probably this question is very simple but I still don't get it... When I used gffcompare to compare stringtie gtf and NCBI annotation gff file. It didn't produce an annotated.gtf file, which marks transcript variations. How can I make it?

NCBI GFF:

##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ASM24018v2
#!genome-build-accession NCBI_Assembly:GCF_000240185.1
##sequence-region NC_016845.1 1 5333942
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1125630
NC_016845.1 RefSeq  region  1   5333942 .   +   .   ID=NC_016845.1:1..5333942;Dbxref=taxon:1125630;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=HS11286;sub-species=pneumoniae
NC_016845.1 RefSeq  gene    382 822 .   -   .   ID=gene-KPHS_00010;Dbxref=GeneID:11849782;Name=KPHS_00010;gbkey=Gene;gene_biotype=protein_coding;locus_tag=KPHS_00010
NC_016845.1 RefSeq  CDS 382 822 .   -   0   ID=cds-YP_005224301.1;Parent=gene-KPHS_00010;Dbxref=Genbank:YP_005224301.1,GeneID:11849782;Name=YP_005224301.1;gbkey=CDS;locus_tag=KPHS_00010;product=flavodoxin;protein_id=YP_005224301.1;transl_table=11
NC_016845.1 RefSeq  gene    922 1380    .   -   .   ID=gene-KPHS_00020;Dbxref=GeneID:11849790;Name=KPHS_00020;gbkey=Gene;gene_biotype=protein_coding;locus_tag=KPHS_00020
NC_016845.1 RefSeq  CDS 922 1380    .   -   0   ID=cds-YP_005224302.1;Parent=gene-KPHS_00020;Dbxref=Genbank:YP_005224302.1,GeneID:11849790;Name=YP_005224302.1;gbkey=CDS;locus_tag=KPHS_00020;product=DNA-binding transcriptional regulator AsnC;protein_id=YP_005224302.1;transl_table=11

Stringtie output:

# stringtie --merge -p 20 -m 200 -G /home/linjuncheng/genome/annotation/Klebsiella_pneumoniae_ASM24018v2_genomic.gff -o stringtie_merged.gtf gtf.list
# StringTie version 2.1.5
NC_016838.1 StringTie   transcript  201 1418    1000    +   .   gene_id "MSTRG.1"; transcript_id "gene-KPHS_p100010"; 
NC_016838.1 StringTie   exon    201 1418    1000    +   .   gene_id "MSTRG.1"; transcript_id "gene-KPHS_p100010"; exon_number "1"; 
NC_016838.1 StringTie   transcript  1870    2696    1000    -   .   gene_id "MSTRG.2"; transcript_id "gene-KPHS_p100020"; 
NC_016838.1 StringTie   exon    1870    2696    1000    -   .   gene_id "MSTRG.2"; transcript_id "gene-KPHS_p100020"; exon_number "1"; 
NC_016838.1 StringTie   transcript  2082    2696    1000    -   .   gene_id "MSTRG.2"; transcript_id "gene-KPHS_p100030"; 
NC_016838.1 StringTie   exon    2082    2696    1000    -   .   gene_id "MSTRG.2"; transcript_id "gene-KPHS_p100030"; exon_number "1"; 
NC_016838.1 StringTie   transcript  2780    2956    1000    -   .   gene_id "MSTRG.3"; transcript_id "gene-KPHS_p100040"; 
NC_016838.1 StringTie   exon    2780    2956    1000    -   .   gene_id "MSTRG.3"; transcript_id "gene-KPHS_p100040"; exon_number "1"; 
NC_016838.1 StringTie   transcript  3127    4473    1000    -   .   gene_id "MSTRG.4"; transcript_id "gene-KPHS_p100050"; 
NC_016838.1 StringTie   exon    3127    4473    1000    -   .   gene_id "MSTRG.4"; transcript_id "gene-KPHS_p100050"; exon_number "1"; 
NC_016838.1 StringTie   transcript  4115    5418    1000    -   .   gene_id "MSTRG.4"; transcript_id "gene-KPHS_p100060"; 

[Pierre Lindenbaum]

save the planet: Just copy-n-paste the text from your terminal, instead of using a screenshot.

[linjc.xmu]

Thanks. I revised it. Do you know how to achieve it?