Question: Why does my GFF3 file not have any exons in the annotation lines read by HTseq-count
0
gravatar for Joey Zou
3 months ago by
Joey Zou0
Joey Zou0 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;
ADD COMMENTlink written 3 months ago by Joey Zou0

Where did you get the file from?

ADD REPLYlink written 3 months ago by Devon Ryan1.9k

Hi,Devon Ryan I got the file from GigaDB --->http://gigadb.org/dataset/view/id/100331/File_page/3 Something problem with this file?

ADD REPLYlink written 3 months ago by Joey Zou0
0
gravatar for Devon Ryan
3 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Yes, it's missing exons. You should ask the authors why this is, since that's quite annoying.

ADD COMMENTlink written 3 months ago by Devon Ryan1.9k
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