src/hg/makeDb/doc/mm9.txt 1.128
1.128 2010/03/16 05:58:17 angie
IKMC Genes (komp) update.
Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.127
retrieving revision 1.128
diff -b -B -U 4 -r1.127 -r1.128
--- src/hg/makeDb/doc/mm9.txt 12 Mar 2010 17:03:25 -0000 1.127
+++ src/hg/makeDb/doc/mm9.txt 16 Mar 2010 05:58:17 -0000 1.128
@@ -8231,14 +8231,15 @@
# loaded by Belinda Giardine, in same manner as hg18 ORegAnno track
############################################################################
-# JAX/MGI TRACKS (DONE 8/20/09 angie)
+# JAX/MGI TRACKS (IN PROGRESS 3/12/10 angie)
+# Previously done 8/20/09 in /hive/data/genomes/mm9/bed/jax/2009_08 (pushed)
# Previously done 6/11/09 in /hive/data/genomes/mm9/bed/jax/2009_06 (pushed)
# Previously done 4/24/09 in /hive/data/genomes/mm9/bed/jax/2009_04 (not pushed)
# Previously done 9/24/08 in /cluster/data/mm9/bed/jax/2008_09
- mkdir -p /hive/data/genomes/mm9/bed/jax/2009_08
- cd /hive/data/genomes/mm9/bed/jax/2009_08
+ mkdir -p /hive/data/genomes/mm9/bed/jax/2010_03
+ cd /hive/data/genomes/mm9/bed/jax/2010_03
wget ftp://ftp.informatics.jax.org/pub/gbrowse/\*
wget ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt
# Jax Rep Transcript track
@@ -8611,20 +8612,21 @@
rm bed.tab
#########################################################################
-# KOMP/IKMC (KNOCKOUT MOUSE PROJECT became Int'l Knockout Mouse Cons) (DONE 12/8/09 angie)
+# KOMP/IKMC (KNOCKOUT MOUSE PROJECT became Int'l Knockout Mouse Cons) (DONE 3/12/10 angie)
+# done 12/8/09 w/files emailed from Carol 12/7
# done 7/24/09 w/files emailed from Carol 7/24
# done 5/7/09 w/files emailed from Carol Bult 5/7
# done 2/12/09 w/files emailed from Carol Bult 2/12
# done 10/21/08 w/files emailed from Carol Bult 10/18
ssh hgwdev
- mkdir -p /hive/data/genomes/mm9/bed/komp/2009_12
- cd /hive/data/genomes/mm9/bed/komp/2009_12
- # Save files emailed from Carol Bult 12/7 as
- # 20091204_ikmc.gff.gz
+ mkdir -p /hive/data/genomes/mm9/bed/komp/2010_03
+ cd /hive/data/genomes/mm9/bed/komp/2010_03
+ # Save files emailed from Carol Bult 3/12 as
+ # 20100312_ikmc.gff.gz
# Make bed12 with itemRgb:
- zcat 20091204_ikmc.gff.gz \
+ zcat 20100312_ikmc.gff.gz \
| perl -we \
'while (<>) { \
s/\r?\n$//; \
($chr, undef, $ctr, $s, $e, undef, undef, undef, $id, $col, $n) = split("\t"); \
@@ -8657,26 +8659,27 @@
print join("\t", $chrom, $chromStart, $chromEnd, $name, 0, ".", $chromStart, \
$chromStart, $color, $blkCount, $blkSizes, $blkStarts) . "\n"; \
}' \
| sort -k 1,1 -k 2n,2n > komp.bed
-#Got 36359 genes.
+#Got 40093 genes.
# No stderr empty-coord warnings this time (no unmapped items).
# Make an alias-style table with associated info (MGI ID and status):
- zcat 20091204_ikmc.gff.gz \
+ zcat 20100312_ikmc.gff.gz \
| perl -wpe 's/\r?\n$//; @w = split("\t"); \
if ($w[3] eq "") { s/^.*//; next; } # Some lines have no coords. \
if ($w[4] <= 0) { s/^.*//; next; } # A few lines have end=0. \
$w[8] =~ m/^(MGI:\d+); (\w+); (\w.*)/ || die; \
($mgi, $designId, $status) = ($1, $2, $3); \
$_ = "$w[10]_$designId\t$mgi,$w[2],$status\n";' \
| sort -u > kompExtra.tab
wc -l kompExtra.tab
-#36359 kompExtra.tab
+#40093 kompExtra.tab
# Load 'em up:
hgLoadBed mm9 komp komp.bed
#Loaded 32185 elements of size 12
hgLoadSqlTab mm9 kompExtra $HOME/kent/src/hg/lib/genericAlias.sql kompExtra.tab
checkTableCoords -verbose=2 mm9 komp
+#mm9.komp item Eif2s1_42274 chr12:79973648-79983000: blocks 3 and 4 overlap.
#mm9.komp item Tekt3_41479 chr11:62887195-62896116: blocks 3 and 4 overlap.
#mm9.komp item Tekt3_41478 chr11:62887195-62896116: blocks 3 and 4 overlap.
#mm9.komp item Tekt3_41477 chr11:62887195-62896116: blocks 3 and 4 overlap.
#mm9.komp item Tekt3_41476 chr11:62887195-62896116: blocks 3 and 4 overlap.
@@ -8686,27 +8689,29 @@
# Note from July '09: Carol noticed some very long items and is asking
# Sanger about them. Here's how to check it ourselves next time:
hgsql mm9 -e 'select name, (chromEnd-chromStart) as length from komp \
where chromEnd - chromStart > 1000000 order by length desc;'
-#+----------------------+----------+
+#+----------------------+-----------+
#| name | length |
-#+----------------------+----------+
+#+----------------------+-----------+
+#| Chrac1_77013 | 100321422 |
#| Ankrd22_67616 | 51920750 |
+#| Sp140_77012 | 2457682 |
#| Ptprd_VG12763 | 2270723 |
-#| Macrod2_VG12650 | 1997658 |
#| A430089I19Rik_71812 | 1814706 |
#| 1700049E17Rik2_68957 | 1596021 |
#| Pcdh15_VG15967 | 1550393 |
#| Gpc5_VG15750 | 1431812 |
-#| Lrrc4c_VG10110 | 1313498 |
#| Agbl4_VG16439 | 1266664 |
#| Prkg1_VG15918 | 1197272 |
+#| Rnaset2b_77193 | 1153790 |
#| Ptprt_VG10147 | 1139158 |
+#| Nrxn1_VG16178 | 1056424 |
#| Ccl21b_67667 | 1019106 |
-#+----------------------+----------+
+#+----------------------+-----------+
runJoiner.csh mm9 komp
-# mm9.kompExtra.name - hits 36359 of 36359 ok
+# mm9.kompExtra.name - hits 40093 of 40093 ok
#########################################################################
### Affy MOE430 version 2 (DONE - 2008-09-25,10-02 - Hiram)