1. Updated the dates in
   /data/wade/resnick/p53chip/hub_Dec2015/hub_NIEHS.txt
   /data/wade/resnick/p53chip/hub_Dec2015/this_hub_url.txt
2. Copied bigBed files from
   /ddn/gs1/home/bennettb/projects/Resnick/15_12_p53/track_hub_update/peaks/out/bigbed_files/*.bigBed
   to
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/.
   (This added color to each peak based on whether it had a p53 motif or not)
3. Copied
   /ddn/gs1/home/bennettb/projects/Resnick/15_12_p53/track_hub_update/peaks/out/trackDb.txt
   to
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.updated.txt
   (This told the track hub to display the color in the bigBed files)
4. Copied bigBed files from
   /ddn/gs1/home/bennettb/projects/Resnick/15_12_p53/track_hub_update/degs/out/bigbed_files/*.bigBed
   to
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/.
   (These are the DEG tracks)
5. Copied
   /ddn/gs1/home/bennettb/projects/Resnick/15_12_p53/track_hub_update/degs/out/trackDb.txt
   to
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.DEGs.txt
   (This is the portion of the track hub for the DEG tracks)
6. Copied and converted microRNA track
   sort -k1,1 -k2,2n /ddn/gs1/home/grimmsa/resnick/p53_chipseq_fullset_Jan2015/META/other_features/microRNA/hsa.hg19-liftover.bed > /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/hsa.hg19-liftover_sorted.bed
   /ddn/gs1/home/bennettb/tools/ucsc/bedToBigBed /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/hsa.hg19-liftover_sorted.bed /ddn/gs1/home/bennettb/references/ucsc/hg19.chromSizes /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/hsa.hg19-liftover.bigBed
   rm -f /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/hsa.hg19-liftover_sorted.bed
7. Copied and converted lincRNA track
   cat /ddn/gs1/home/grimmsa/resnick/p53_chipseq_fullset_Jan2015/META/other_features/lincRNA/lincRNAs_transcripts.gtf | /ddn/gs1/home/bennettb/tools/ucsc/gtfToGenePred stdin stdout | /ddn/gs1/home/bennettb/tools/ucsc/genePredToBed | sort -k1,1 -k2,2n - > /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/lincRNAs_transcripts_sorted.bed
   /ddn/gs1/home/bennettb/tools/ucsc/bedToBigBed /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/lincRNAs_transcripts_sorted.bed /ddn/gs1/home/bennettb/references/ucsc/hg19.chromSizes /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/lincRNAs_transcripts.bigBed
   rm -f /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/lincRNAs_transcripts_sorted.bed
8. Downloaded the FANTOM5 enhancers track
   http://fantom.gsc.riken.jp/5/datahub/hg19/enhancers/human_permissive_enhancers_phase_1_and_2.bb
   to
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/human_permissive_enhancers_phase_1_and_2.bb
9. Created
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.RNA.txt
   (This is the portion of the track hub for the microRNA, lincRNA, and FANTOM5 enhancers tracks)
10. Concatenated the trackDb.txt files
   cat /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.updated.txt /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.DEGs.txt /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.RNA.txt > /data/wade/resnick/p53chip/hub_Dec2015/hg19/trackDb.txt
11. Manually changed three lines with "IMR90_sensescent_p53_Lowe.exprDirection" to "IMR90_senescent_p53_Lowe.exprDirection"
12. Manually changed in trackDb.txt
   longLabel "Depth for Input Associated with ChIP-seq Datasets" -> "Input depth associated with human p53 ChIP-seq datasets"
   longLabel "Expression" -> "Differential gene expression associated with human p53 ChIP-seq datasets"
13. Created a bigBed with a single peak at chrM:0-0 and replaced
   /data/wade/resnick/p53chip/hub_Dec2015/hg19/DATA/IMR90_growing_p53_Narita.sissrs-peakcalls.min200.bigBed
14. Manually changed for "IMR90_growing_p53_Narita.P" track in trackDb.txt
   type "bigBed 3" -> "bigBed 9"
   Add: "itemRgb On"