Question: Why does my GFF3 file not have any exons in the annotation lines read by HTseq-count
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Joey Zou • 0 wrote:
When I ran htseq-count with my data. I am getting the error:
Warning: No features of type 'exon' found.
Warning: Read E00488:175:H3CYCCCXY:3:1101:1610:63173 claims to have an aligned mate which could not be found in an adjacent line.
Warning: 2235041 reads with missing mate encountered.
I don't konw if the gff file was broken or something problem, and I should need to convert GFF file to GTF file? . My gff files looks like the following below:
scaffold1002 GLEAN mRNA 20257 25173 0.970574 + . ID=DUH000001.2;source_id=RHOqdgD_GLEAN_10019967;
scaffold1002 GLEAN CDS 20257 20352 . + 0 Parent=DUH000001.2;
scaffold1002 GLEAN CDS 20458 20579 . + 0 Parent=DUH000001.2;
scaffold1002 GLEAN CDS 20917 21050 . + 1 Parent=DUH000001.2;
scaffold1002 GLEAN CDS 21578 21728 . + 2 Parent=DUH000001.2;
scaffold1002 GLEAN CDS 22844 23115 . + 1 Parent=DUH000001.2;
scaffold1002 GLEAN CDS 24360 24475 . + 2 Parent=DUH000001.2;
scaffold1002 GLEAN CDS 24871 25173 . + 0 Parent=DUH000001.2;
scaffold1002 Cuff mRNA 29262 31510 1000 + . ID=DUH000002.1;source_id=CUFF1.6.1;
scaffold1002 Cuff UTR_5 29262 29749 1000 + . Parent=DUH000002.1;support_id=CUFF1.6.1;
scaffold1002 Cuff CDS 29750 31108 1000 + 0 Parent=DUH000002.1;
scaffold1002 Cuff UTR_3 31109 31510 1000 + . Parent=DUH000002.1;support_id=CUFF1.6.1;
scaffold1002 Cuff mRNA 78137 83175 1000 + . ID=DUH000003.1;source_id=CUFF1.7.1;
scaffold1002 Cuff UTR_5 81341 81400 1000 + . Parent=DUH000003.1;support_id=CUFF1.7.1;
scaffold1002 Cuff CDS 81401 81403 1000 + 0 Parent=DUH000003.1;
scaffold1002 Cuff CDS 82430 82660 1000 + 0 Parent=DUH000003.1;
scaffold1002 Cuff UTR_3 82661 83175 1000 + . Parent=DUH000003.1;support_id=CUFF1.7.1;
scaffold1002 GLEAN mRNA 83372 84043 0.696261 - . ID=DUH000004.1;source_id=RHOqdgD_GLEAN_10019968;part_support_id=CUFF1.8.1;
scaffold1002 GLEAN CDS 83372 84043 . - 0 Parent=DUH000004.1;
scaffold1002 GLEAN mRNA 106002 106979 0.601731 + . ID=DUH000005.1;source_id=RHOqdgD_GLEAN_10019969;
scaffold1002 GLEAN CDS 106002 106271 . + 0 Parent=DUH000005.1;
scaffold1002 GLEAN CDS 106932 106979 . + 0 Parent=DUH000005.1;
scaffold1002 GLEAN mRNA 110342 111616 0.993352 - . ID=DUH000006.1;source_id=RHOqdgD_GLEAN_10019970;
scaffold1002 GLEAN CDS 111600 111616 . - 0 Parent=DUH000006.1;
scaffold1002 GLEAN CDS 110990 111140 . - 1 Parent=DUH000006.1;
scaffold1002 GLEAN CDS 110769 110920 . - 0 Parent=DUH000006.1;
scaffold1002 GLEAN CDS 110342 110495 . - 1 Parent=DUH000006.1;
scaffold1002 GLEAN mRNA 120973 124224 0.84899 - . ID=DUH000007.3;source_id=RHOqdgD_GLEAN_10019971;
scaffold1002 GLEAN CDS 123621 124224 . - 0 Parent=DUH000007.3;
scaffold1002 GLEAN CDS 122137 122587 . - 2 Parent=DUH000007.3;
scaffold1002 GLEAN CDS 120973 121387 . - 1 Parent=DUH000007.3;
scaffold1002 Cuff mRNA 161274 166792 1000 - . ID=DUH000008.1;source_id=CUFF1.536.1;
scaffold1002 Cuff UTR_5 164124 166792 1000 - . Parent=DUH000008.1;support_id=CUFF1.536.1;
Where did you get the file from?
Hi，Devon Ryan I got the file from GigaDB --->http://gigadb.org/dataset/view/id/100331/File_page/3 Something problem with this file?