alignment track not showing anything

[szechp]

i wanted to add an alignment track, it comes as gff3, i prepared it as instructed but it doesnt show alignments. does this only work when the alignments come in a bam file?

[cmdcolin]

Do you have any snippet of the GFF3? The alignments track is highly optimized for BAM and CRAM but it might be possible to support other formats.

[szechp]

with snippet you mean a sample of the files content?
is there a way to get bam files from gff3's?

[szechp]

##gff-version   3
# Generated by GMAP version 2019-06-10 using call:  gmapl.sse2 -D ./index/genome_index -d Abal.1_1.gmap -f gff3_gene --nthreads=16 --min-intronlength=9 --min-trimmed-coverage=0.95 --min-identity=0.95 -n1 /isg/treegenes/treegenes_store/FTP/Transcriptome/TSA_Frame_Selected/Abal/Abal_TSA.fasta
aalba5_s00382444	Abal.1_1.gmap	gene	1100	1603	.	+	.	ID=JV157082.1.path1;Name=JV157082.1
aalba5_s00382444	Abal.1_1.gmap	mRNA	1100	1603	.	+	.	ID=JV157082.1.mrna1;Name=JV157082.1;Parent=JV157082.1.path1;coverage=95.6;identity=100.0;matches=504;mismatches=0;indels=0;unknowns=0
aalba5_s00382444	Abal.1_1.gmap	exon	1100	1603	100	+	.	ID=JV157082.1.mrna1.exon1;Name=JV157082.1;Parent=JV157082.1.mrna1;Target=JV157082.1 527 24 .
aalba5_s00382444	Abal.1_1.gmap	CDS	1100	1261	100	+	0	ID=JV157082.1.mrna1.cds1;Name=JV157082.1;Parent=JV157082.1.mrna1;Target=JV157082.1 185 24 .
###
aalba5_s00059732	Abal.1_1.gmap	gene	29993	30505	.	+	.	ID=JV157077.1.path1;Name=JV157077.1
aalba5_s00059732	Abal.1_1.gmap	mRNA	29993	30505	.	+	.	ID=JV157077.1.mrna1;Name=JV157077.1;Parent=JV157077.1.path1;coverage=98.1;identity=99.6;matches=512;mismatches=0;indels=2;unknowns=0
aalba5_s00059732	Abal.1_1.gmap	exon	29993	30505	99	+	.	ID=JV157077.1.mrna1.exon1;Name=JV157077.1;Parent=JV157077.1.mrna1;Target=JV157077.1 523 11 .
aalba5_s00059732	Abal.1_1.gmap	CDS	30404	30504	99	+	0	ID=JV157077.1.mrna1.cds1;Name=JV157077.1;Parent=JV157077.1.mrna1;Target=JV157077.1 522 421 .
###
aalba5_s00002740	Abal.1_1.gmap	gene	39050	40920	.	+	.	ID=JV157073.1.path1;Name=JV157073.1
aalba5_s00002740	Abal.1_1.gmap	mRNA	39050	40920	.	+	.	ID=JV157073.1.mrna1;Name=JV157073.1;Parent=JV157073.1.path1;coverage=100.0;identity=100.0;matches=561;mismatches=0;indels=0;unknowns=0
aalba5_s00002740	Abal.1_1.gmap	exon	39050	39114	100	+	.	ID=JV157073.1.mrna1.exon1;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 1 65 +
aalba5_s00002740	Abal.1_1.gmap	exon	39213	39338	100	+	.	ID=JV157073.1.mrna1.exon2;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 66 191 +
aalba5_s00002740	Abal.1_1.gmap	exon	39435	39620	100	+	.	ID=JV157073.1.mrna1.exon3;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 192 377 +
aalba5_s00002740	Abal.1_1.gmap	exon	39918	40031	100	+	.	ID=JV157073.1.mrna1.exon4;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 378 491 +
aalba5_s00002740	Abal.1_1.gmap	exon	40851	40920	100	+	.	ID=JV157073.1.mrna1.exon5;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 492 561 +
aalba5_s00002740	Abal.1_1.gmap	CDS	39052	39114	100	+	0	ID=JV157073.1.mrna1.cds1;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 3 65 +
aalba5_s00002740	Abal.1_1.gmap	CDS	39213	39338	100	+	0	ID=JV157073.1.mrna1.cds2;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 66 191 +
aalba5_s00002740	Abal.1_1.gmap	CDS	39435	39620	100	+	0	ID=JV157073.1.mrna1.cds3;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 192 377 +
aalba5_s00002740	Abal.1_1.gmap	CDS	39918	40031	100	+	0	ID=JV157073.1.mrna1.cds4;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 378 491 +
aalba5_s00002740	Abal.1_1.gmap	CDS	40851	40919	100	+	0	ID=JV157073.1.mrna1.cds5;Name=JV157073.1;Parent=JV157073.1.mrna1;Target=JV157073.1 492 560 +

[cmdcolin]

Gotcha. We don't technically support (or specifically, we dont do anything with) the target field in gff. You could load it as a gff3tabix track anyways tho

[szechp]

thats what i did and its just blank then...

[cmdcolin]

If you navigate to e.g.

aalba5_s00382444:1000-2000

in the browser, it should show this gene

aalba5_s00382444	Abal.1_1.gmap	gene	1100	1603	.	+	.	ID=JV157082.1.path1;Name=JV157082.1
aalba5_s00382444	Abal.1_1.gmap	mRNA	1100	1603	.	+	.	ID=JV157082.1.mrna1;Name=JV157082.1;Parent=JV157082.1.path1;coverage=95.6;identity=100.0;matches=504;mismatches=0;indels=0;unknowns=0
aalba5_s00382444	Abal.1_1.gmap	exon	1100	1603	100	+	.	ID=JV157082.1.mrna1.exon1;Name=JV157082.1;Parent=JV157082.1.mrna1;Target=JV157082.1 527 24 .
aalba5_s00382444	Abal.1_1.gmap	CDS	1100	1261	100	+	0	ID=JV157082.1.mrna1.cds1;Name=JV157082.1;Parent=JV157082.1.mrna1;Target=JV157082.1 185 24 .