[ensembl-dev] version 91 error report

Hiram Clawson hiram at soe.ucsc.edu
Thu Dec 21 19:10:04 GMT 2017


Good Morning Ensembl Gene Fans:

As I transfer the Ensembl gene definitions to the UCSC genome browser,
there are sometimes a few difficulties with a few of the annotations.
Mostly in the newly released genome annotations.  Please note below
the anomalies I find in the version 91 release for 17 of the sequences.

To move forward on these, I drop these few annotations as they are
transferred into the UCSC genome browser.  These annotations can
be seen in the genome-test.soe.ucsc.ed browser for the assemblies:

aotNan1 felCat8 gorGor4 jacJac1 macFas5 manLeu1 mesAur1 micMur3 nanGal1
octDeg1 panPan2 panTro5 proCoq1 rhiBie1 rhiRox1 saiBol1 tarSyr2

These errors can be found from the Ensembl gtf.gz file via the process:
   gtfToGenePred ensembl.gtf.gz ucscGenePred.gp
   genePredCheck -chromSizes=chrom.sizes ucscGenePred.gp

Where chrom.sizes can be created from:
   faToTwoBit ensembl.dna.toplevel.fa.gz ensembl.2bit
   twoBitInfo ensembl.2bit stdout | sort -k2,2nr > chrom.sizes

--Hiram

=== Aotus_nancymaae.Anan_2.0.91.gtf.gz
ENSANAT00000008002.1 txEnd 21157 >= chromSize 21156
ENSANAT00000018995.1 txEnd 11710 >= chromSize 11706
ENSANAT00000001044.1 txEnd 9860 >= chromSize 9850
ENSANAT00000005144.1 txEnd 3639 >= chromSize 3636
checked: 50016 failed: 4
============================================

=== Felis_catus.Felis_catus_8.0.91.gtf.gz
ENSFCAT00000040388.1 txEnd 851 >= chromSize 830
ENSFCAT00000022232.2 txEnd 778 >= chromSize 777
ENSFCAT00000046539.1 txEnd 618 >= chromSize 615
ENSFCAT00000038331.1 txEnd 621 >= chromSize 602
ENSFCAT00000042688.1 txEnd 616 >= chromSize 602
ENSFCAT00000042073.1 txEnd 561 >= chromSize 559
ENSFCAT00000035557.1 txEnd 538 >= chromSize 533
ENSFCAT00000042534.1 txEnd 536 >= chromSize 533
checked: 34879 failed: 8
============================================

=== Gorilla_gorilla.gorGor4.91.gtf.gz
ENSGGOT00000040833.2 txEnd 2008 >= chromSize 2000
ENSGGOT00000066834.1 txEnd 2009 >= chromSize 2000
ENSGGOT00000065889.1 txEnd 1325 >= chromSize 1322
ENSGGOT00000041741.2 txEnd 923 >= chromSize 913
ENSGGOT00000064312.1 txEnd 900 >= chromSize 894
ENSGGOT00000042831.1 txEnd 872 >= chromSize 870
ENSGGOT00000039360.2 txEnd 831 >= chromSize 818
checked: 52960 failed: 7
============================================

=== Jaculus_jaculus.JacJac1.0.91.gtf.gz
ENSJJAT00000007476.1 txEnd 4410 >= chromSize 4389
ENSJJAT00000002946.1 txEnd 1935 >= chromSize 1923
checked: 31768 failed: 2
============================================

=== Macaca_fascicularis.Macaca_fascicularis_5.0.91.gtf.gz
ENSMFAT00000049321.1 txEnd 5011 >= chromSize 5009
checked: 53156 failed: 1
============================================

=== Mandrillus_leucophaeus.Mleu.le_1.0.91.gtf.gz
ENSMLET00000030838.1 txEnd 35289 >= chromSize 35264
checked: 47765 failed: 1
============================================

=== Mesocricetus_auratus.MesAur1.0.91.gtf.gz
ENSMAUT00000008954.1 txEnd 18377 >= chromSize 18369
ENSMAUT00000008838.1 txEnd 1152 >= chromSize 1150
checked: 29936 failed: 2
============================================

=== Microcebus_murinus.Mmur_3.0.91.gtf.gz
ENSMICT00000068593.1 txEnd 5528 >= chromSize 5525
ENSMICT00000068583.1 txEnd 4860 >= chromSize 4858
ENSMICT00000039077.2 txEnd 4792 >= chromSize 4790
ENSMICT00000052172.2 txEnd 2742 >= chromSize 2739
ENSMICT00000049755.2 txEnd 1553 >= chromSize 1539
ENSMICT00000068718.1 txEnd 1264 >= chromSize 1261
checked: 44024 failed: 6
============================================

=== Nannospalax_galili.S.galili_v1.0.91.gtf.gz
ENSNGAT00000010911.1 txEnd 1279026 >= chromSize 1279023
ENSNGAT00000011043.1 txEnd 3095 >= chromSize 3068
ENSNGAT00000005613.1 txEnd 883 >= chromSize 874
ENSNGAT00000005469.1 txEnd 843 >= chromSize 822
ENSNGAT00000003195.1 txEnd 661 >= chromSize 657
ENSNGAT00000004333.1 txEnd 660 >= chromSize 631
ENSNGAT00000010598.1 txEnd 588 >= chromSize 564
ENSNGAT00000004053.1 txEnd 491 >= chromSize 488
ENSNGAT00000004795.1 txEnd 337 >= chromSize 334
ENSNGAT00000008686.1 txEnd 245 >= chromSize 238
checked: 32861 failed: 10
============================================

=== Octodon_degus.OctDeg1.0.91.gtf.gz
ENSODET00000030480.1 txEnd 10465 >= chromSize 10456
checked: 32968 failed: 1
============================================

=== Pan_paniscus.panpan1.1.91.gtf.gz
ENSPPAT00000007687.1 txEnd 2172 >= chromSize 2168
checked: 50791 failed: 1
============================================

=== Pan_troglodytes.Pan_tro_3.0.91.gtf.gz
ENSPTRT00000103531.1 txEnd 10764 >= chromSize 10756
ENSPTRT00000079867.1 txEnd 1416 >= chromSize 1400
ENSPTRT00000096982.1 txEnd 1326 >= chromSize 1310
checked: 58366 failed: 3
============================================

=== Propithecus_coquereli.Pcoq_1.0.91.gtf.gz
ENSPCOT00000008378.1 txEnd 14532 >= chromSize 14529
checked: 37912 failed: 1
============================================

=== Rhinopithecus_bieti.ASM169854v1.91.gtf.gz
ENSRBIT00000004729.1 txEnd 1295 >= chromSize 1287
ENSRBIT00000004240.1 txEnd 925 >= chromSize 896
ENSRBIT00000007958.1 txEnd 874 >= chromSize 870
ENSRBIT00000005433.1 txEnd 499 >= chromSize 496
ENSRBIT00000004757.1 txEnd 492 >= chromSize 474
checked: 50868 failed: 5
============================================

=== Rhinopithecus_roxellana.Rrox_v1.91.gtf.gz
ENSRROT00000015658.1 txEnd 2904 >= chromSize 2895
ENSRROT00000003328.1 txEnd 575 >= chromSize 551
ENSRROT00000003014.1 txEnd 553 >= chromSize 550
ENSRROT00000017963.1 txEnd 425 >= chromSize 423
ENSRROT00000004422.1 txEnd 409 >= chromSize 406
ENSRROT00000005493.1 txEnd 247 >= chromSize 235
ENSRROT00000010204.1 txEnd 233 >= chromSize 229
ENSRROT00000009486.1 txEnd 223 >= chromSize 220
ENSRROT00000000177.1 txEnd 217 >= chromSize 214
checked: 53209 failed: 9
============================================

=== Saimiri_boliviensis_boliviensis.SaiBol1.0.91.gtf.gz
ENSSBOT00000006176.1 txEnd 1192 >= chromSize 1189
checked: 48403 failed: 1
============================================

=== Carlito_syrichta.Tarsius_syrichta-2.0.1.91.gtf.gz
ENSTSYT00000036298.1 txEnd 9974 >= chromSize 9960
ENSTSYT00000025862.1 txEnd 865 >= chromSize 863
ENSTSYT00000041648.1 txEnd 480 >= chromSize 479
ENSTSYT00000046606.1 txEnd 454 >= chromSize 452
checked: 38314 failed: 4
============================================





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