Cufflinks missing GTF features

[h_manoj]

Hello,

I had run cufflinks using Gencode M2 annotation. I see that 1,073 features that are present in the GTF file are not present in the cufflinks output (no errors, no LOWDATA, HIDATA, FAIL messages).

However, when I extract the GTF features for these missing cases, cufflinks quantifies FPKM levels.

For eg., gene Cyba:
When I run the whole Gencode M2 annotation, I do not see any record with Cyba in the cufflinks output.
But with just the missing features, I get the following results:

UnfoundFeats_CflnksOUT_Sample1/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 5.6723 4.77636 6.57062 OK
UnfoundFeats_CflnksOUT_Sample2/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 7.6306 6.46357 8.7991 OK
UnfoundFeats_CflnksOUT_Sample3/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 4.71393 3.88789 5.53909 OK
UnfoundFeats_CflnksOUT_Sample4/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 8.86488 7.67735 10.0541 OK
UnfoundFeats_CflnksOUT_Sample5/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 8.87608 7.7003 10.0601 OK
UnfoundFeats_CflnksOUT_Sample6/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 7.74688 6.64262 8.85341 OK
UnfoundFeats_CflnksOUT_Sample7/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 6.78283 5.76969 7.8051 OK
UnfoundFeats_CflnksOUT_Sample8/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 7.3683 6.30266 8.43726 OK
UnfoundFeats_CflnksOUT_Sample9/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 7.08729 6.06264 8.11498 OK
UnfoundFeats_CflnksOUT_Sample10/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 7.32592 6.32091 8.33407 OK
UnfoundFeats_CflnksOUT_Sample11/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 6.37045 5.43803 7.30236 OK
UnfoundFeats_CflnksOUT_Sample12/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 6.54227 5.54556 7.53957 OK
UnfoundFeats_CflnksOUT_Sample13/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 6.71044 5.6797 7.74345 OK
UnfoundFeats_CflnksOUT_Sample14/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 7.01325 6.00119 8.02714 OK
UnfoundFeats_CflnksOUT_Sample15/genes.fpkm_tracking:ENSMUSG00000006519.10 - - ENSMUSG00000006519.10 Cyba - chr8:122424771-122432940 - - 8.12649 7.03826 9.21508 OK


I don't think there is anything complicated in the gene structure (as seen in UCSC genome browser) -- no overlapping genes, no mis-annotation etc.

Hope the developers or other experts can comment on this issue.

Thanks very much,
Regards,
Manoj.


More information:

In UCSC genome browser: mm10: chr8:122,422,729-122,434,983

http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position=chr8%3A122422729-122434983&hgsid=373549907_cCeNONAQDkZuIzBiXtaClJXALLR8

GTF file containing Cyba gene from Gencode M2 annotation:
chr8 ENSEMBL gene 122424772 122432940 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUSG00000006519.10"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba"; level 3;
chr8 ENSEMBL transcript 122424772 122432940 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL exon 122432810 122432940 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 1; exon_id "ENSMUSE00000913389.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL CDS 122432810 122432867 . - 0 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 1; exon_id "ENSMUSE00000913389.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL start_codon 122432865 122432867 . - 0 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 1; exon_id "ENSMUSE00000913389.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL exon 122427655 122427724 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 2; exon_id "ENSMUSE00000215062.3"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL CDS 122427655 122427724 . - 2 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 2; exon_id "ENSMUSE00000215062.3"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL exon 122427229 122427303 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 3; exon_id "ENSMUSE00000215063.3"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL CDS 122427229 122427303 . - 1 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 3; exon_id "ENSMUSE00000215063.3"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL exon 122426936 122427019 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 4; exon_id "ENSMUSE00000298723.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL CDS 122426936 122427019 . - 1 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 4; exon_id "ENSMUSE00000298723.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL exon 122426186 122426267 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 5; exon_id "ENSMUSE00000215060.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL CDS 122426186 122426267 . - 1 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 5; exon_id "ENSMUSE00000215060.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL exon 122424772 122425087 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 6; exon_id "ENSMUSE00000910774.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL CDS 122424881 122425087 . - 0 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 6; exon_id "ENSMUSE00000910774.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL stop_codon 122424878 122424880 . - 0 gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; exon_number 6; exon_id "ENSMUSE00000910774.1"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL UTR 122432868 122432940 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";
chr8 ENSEMBL UTR 122424772 122424880 . - . gene_id "ENSMUSG00000006519.10"; transcript_id "ENSMUST00000017604.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Cyba"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "Cyba-201"; level 3; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS22737.1";