yes, the alignment looks very good using IGV- I think, there is an issue in the GFF file as genes do not appear annotated using IGV (only the sequence appear without gene annotation), do not know how to fix the gff file?
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>complete genome
NC_022544.1 RefSeq region 1 4814801 . + . ID=id0;Dbxref=taxon:568709;Is_circular=true;gbkey=Src;genome=genomic;mol_type=genomic DNA;serovar=Typhimurium;strain=DT2;sub-species=enterica
NC_022544.1 RefSeq gene 169 255 . + . ID=gene0;Name=thrL;Dbxref=GeneID:17155329;gbkey=Gene;gene=thrL;locus_tag=STMDT2_00011
NC_022544.1 RefSeq CDS 169 255 . + 0 ID=cds0;Name=YP_008642919.1;Parent=gene0;Dbxref=Genbank:YP_008642919.1,GeneID:17155329;gbkey=CDS;product=thr operon leader peptide;protein_id=YP_008642919.1;transl_table=11
NC_022544.1 RefSeq gene 337 2799 . + . ID=gene1;Name=thrA;Dbxref=GeneID:17159252;gbkey=Gene;gene=thrA;locus_tag=STMDT2_00021
NC_022544.1 RefSeq CDS 337 2799 . + 0 ID=cds1;Name=YP_008642920.1;Parent=gene1;Dbxref=Genbank:YP_008642920.1,GeneID:17159252;gbkey=CDS;product=aspartokinase I%2Fhomoserine dehydrogenase I;protein_id=YP_008642920.1;transl_table=11
NC_022544.1 RefSeq gene 2801 3730 . + . ID=gene2;Name=thrB;Dbxref=GeneID:17159249;gbkey=Gene;gene=thrB;locus_tag=STMDT2_00031
NC_022544.1 RefSeq CDS 2801 3730 . + 0 ID=cds2;Name=YP_008642921.1;Parent=gene2;Dbxref=Genbank:YP_008642921.1,GeneID:17159249;gbkey=CDS;product=Homoserine kinase;protein_id=YP_008642921.1;transl_table=11
NC_022544.1 RefSeq gene 3734 5020 . + . ID=gene3;Name=thrC;Dbxref=GeneID:17159250;gbkey=Gene;gene=thrC;locus_tag=STMDT2_00041
NC_022544.1 RefSeq CDS 3734 5020 . + 0 ID=cds3;Name=YP_008642922.1;Parent=gene3;Dbxref=Genbank:YP_008642922.1,GeneID:17159250;gbkey=CDS;product=threonine synthase;protein_id=YP_008642922.1;transl_table=11
NC_022544.1 RefSeq gene 5114 5887 . - . ID=gene4;Name=yaaA;Dbxref=GeneID:17159251;gbkey=Gene;gene=yaaA;locus_tag=STMDT2_00051
NC_022544.1 RefSeq CDS 5114 5887 . - 0 ID=cds4;Name=YP_008642923.1;Parent=gene4;Dbxref=Genbank:YP_008642923.1,GeneID:17159251;gbkey=CDS;product=hypothetical protein;protein_id=YP_008642923.1;transl_table=11
NC_022544.1 RefSeq gene 5966 7396 . - . ID=gene5;Name=yaaJ;Dbxref=GeneID:17159391;gbkey=Gene;gene=yaaJ;locus_tag=STMDT2_00061
NC_022544.1 RefSeq CDS 5966 7396 . - 0 ID=cds5;Name=YP_008642924.1;Parent=gene5;Dbxref=Genbank:YP_008642924.1,GeneID:17159391;gbkey=CDS;product=putative amino-acid transport protein;protein_id=YP_008642924.1;transl_table=11
NC_022544.1 RefSeq gene 7665 8618 . + . ID=gene6;Name=talB;Dbxref=GeneID:17159395;gbkey=Gene;gene=talB;locus_tag=STMDT2_00071
NC_022544.1 RefSeq CDS 7665 8618 . + 0 ID=cds6;Name=YP_008642925.1;Parent=gene6;Dbxref=Genbank:YP_008642925.1,GeneID:17159395;gbkey=CDS;product=transaldolase B;protein_id=YP_008642925.1;transl_table=11
NC_022544.1 RefSeq gene 8729 9319 . + . ID=gene7;Name=mog;Dbxref=GeneID:17159215;gbkey=Gene;gene=mog;locus_tag=STMDT2_00081
NC_022544.1 RefSeq CDS 8729 9319 . + 0 ID=cds7;Name=YP_008642926.1;Parent=gene7;Dbxref=Genbank:YP_008642926.1,GeneID:17159215;gbkey=CDS;product=molybdopterin biosynthesis Mog protein;protein_id=YP_008642926.1;transl_table=11
NC_022544.1 RefSeq gene 9376 9942 . - . ID=gene8;Name=yaaH;Dbxref=GeneID:17158379;gbkey=Gene;gene=yaaH;locus_tag=STMDT2_00091
NC_022544.1 RefSeq CDS 9376 9942 . - 0
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Can you remove the fist line from the file (please make a backup copy of original file in case something goes wrong)
Code:>complete genome
To make it a gff3 format file you will have to replace that first line with following two lines http://www.sequenceontology.org/gff3.shtml
Code:##gff-version 3 ##sequence-region NC_022544.1 1 4814801
Last edited by GenoMax; 12-04-2013, 06:08 AM.
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Have you renamed the GFF file as "your_file_name.gff3"?
IGV expects the GFF3 files to have that extension (http://www.broadinstitute.org/software/igv/GFF) and they also need to be tab-delimited (which your example above does not appear to be).
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After taking out the first two lines from your example, adding the two lines for GFF3 meta-data and then converting to tab-delimited text the file appears to work with IGV.
Take these two lines out:
Code:>complete genome NC_022544.1 RefSeq region 1 4814801 . + . ID=id0;Dbxref=taxon:568709;Is_circular=true;gbkey=Src;genome=genomic;mol_type=genomic DNA;serovar=Typhimurium;strain=DT2;sub-species=enterica
Code:##gff-version 3 ##sequence-region NC_022544.1 1 4814801
Attached Files
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how do you convert text (gff3) to tab-delimited, please?
I used:
awk '{ for(i=1;i<=NF;i++){if(i==NF){printf("%s\n",$NF);}else {printf("%s\t",$i)}}}' file.gff3
but did not convert the file to tab-delimited????
##gff-version 3
##sequence-region NC_022544.1 1 4814801
NC_022544.1 RefSeq gene 169 255 . + . ID=gene0;Name=thrL;Dbxref=GeneID:17155329;gbkey=Gene;gene=thrL;locus_tag=STMDT2_00011
NC_022544.1 RefSeq CDS 169 255 . + 0 ID=cds0;Name=YP_008642919.1;Parent=gene0;Dbxref=Genbank:YP_008642919.1,GeneID:17155329;gbkey=CDS;gene=thrL;product=thr operon leader peptide;protein_id=YP_008642919.1;transl_table=11
NC_022544.1 RefSeq gene 337 2799 . + . ID=gene1;Name=thrA;Dbxref=GeneID:17159252;gbkey=Gene;gene=thrA;locus_tag=STMDT2_00021
NC_022544.1 RefSeq CDS 337 2799 . + 0 ID=cds1;Name=YP_008642920.1;Parent=gene1;Dbxref=Genbank:YP_008642920.1,GeneID:17159252;gbkey=CDS;gene=thrA;product=aspartokinase I%2Fhomoserine dehydrogenase I;protein_id=YP_008642920.1;transl_table=11
NC_022544.1 RefSeq gene 2801 3730 . + . ID=gene2;Name=thrB;Dbxref=GeneID:17159249;gbkey=Gene;gene=thrB;locus_tag=STMDT2_00031
NC_022544.1 RefSeq CDS 2801 3730 . + 0 ID=cds2;Name=YP_008642921.1;Parent=gene2;Dbxref=Genbank:YP_008642921.1,GeneID:17159249;gbkey=CDS;gene=thrB;product=Homoserine kinase;protein_id=YP_008642921.1;transl_table=11
NC_022544.1 RefSeq gene 3734 5020 . + . ID=gene3;Name=thrC;Dbxref=GeneID:17159250;gbkey=Gene;gene=thrC;locus_tag=STMDT2_00041
NC_022544.1 RefSeq CDS 3734 5020 . + 0 ID=cds3;Name=YP_008642922.1;Parent=gene3;
Comment
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Try this unix command. Adjust the file names accordingly.
Code:$ tr ' ' \\t < original.gff3 > tab_converted.gff3
Best to put the two top metadata lines in after the conversion.
Comment
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thanks you soo much for your advice and time. managed to view genes on IGV and have got a coverage.txt file showing genes that are covered/ missed from the reference
but have a very simple technichal issue when I open the coverage.txt using excel or libreoffice- I could not sort the coverage values in ascending order as values are written on a separte line
NC_022544.1 RefSeq gene 2096621 2097676 . - . ID=gene2037;Name=cbiG;Dbxref=GeneID:17157414;gbkey=Gene;gene=cbiG;locus_tag=STMDT2_20011
2505 1056 1056 1
NC_022544.1 RefSeq CDS 2096621 2097676 . - 0 "ID=cds1963;Name=YP_008644883.1;Parent=gene2037;Dbxref=Genbank:YP_008644883.1,GeneID:17157414;gbkey=CDS;gene=cbiG;product=cobalamin biosynthesis protein;protein_id=YP_008644883.1;transl_table=11"
2505 1056 1056 0.9
NC_022544.1 RefSeq gene 3145124 3146200 . - . ID=gene2977;Name=STMDT2_29251;Dbxref=GeneID:17156485;gbkey=Gene;locus_tag=STMDT2_29251
1716 1077 1077 0.6
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NC_022544.1 RefSeq gene 2096621 2097676 0 - 0 ID=gene2037;Name=cbiG;Dbxref=GeneID:17157414;gbkey=Gene;gene=cbiG;locus_tag=STMDT2_20011
2505 1056 1056 1 NC_022544.1 RefSeq CDS 2096621
2505 1056 1056 1
NC_022544.1 RefSeq gene 3145124 3146200 0 - 0 ID=gene2977;Name=STMDT2_29251;Dbxref=GeneID:17156485;gbkey=Gene;locus_tag=STMDT2_29251
1716 1077 1077 1 NC_022544.1 RefSeq CDS 3145124
1716 1077 1077 1
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