sam2wig

/bin/sh /share/apps/corona/bin/pipelinesam2wig.sh -Dlog.file=./B6D2F1.log -i B6D2F1.bam -s 24 -v 0 -o B6D2F1 -b wigwam -w true -m unique -c 3

UCSC RNAseq

Brain_eye_log2
track type=bigWig name="Plus eye B6" description="mRNA expression of eye in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6_eye_positive_log2.bw
track type=bigWig name="Minus eye B6" description="mRNA expression of eye in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6_eye_negative_log2.bw
track type=bigWig name="Plus eye D2" description="mRNA expression of eye in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2_eye_positive_log2.bw
track type=bigWig name="Minus eye D2" description="mRNA expression of eye in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2_eye_negative_log2.bw
track type=bigWig name="Plus brain B6" description="mRNA expression of whole brain in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6.negative.wig_all.bw
track type=bigWig name="Minus brain B6" description="mRNA expression of whole brain in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6.positive.wig_all.bw
track type=bigWig name="Plus brain D2" description="mRNA expression of whole brain in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2.negative.wig_all.bw
track type=bigWig name="Minus brain D2" description="mRNA expression of whole brain in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2.positive.wig_all.bw
track type=bigWig name="Plus brain F1" description="mRNA expression of whole brain in F1" visibility=hide color=0,0,200 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/F1.negative.wig_all.bw
track type=bigWig name="Minus brain F1" description="mRNA expression of whole brain in F1" visibility=hide color=0,0,200 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/F1.positive.wig_all.bw


eye_RNAseq_log2
track type=bigWig name="Plus eye B6" description="mRNA expression of eye in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6_eye_positive_log2.bw
track type=bigWig name="Minus eye B6" description="mRNA expression of eye in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6_eye_negative_log2.bw
track type=bigWig name="Plus eye D2" description="mRNA expression of eye in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2_eye_positive_log2.bw
track type=bigWig name="Minus eye D2" description="mRNA expression of eye in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2_eye_negative_log2.bw

RNAseq_Brain_Log
track type=bigWig name="Plus brain B6" description="mRNA expression of whole brain in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6.negative.wig_all.bw
track type=bigWig name="Minus brain B6" description="mRNA expression of whole brain in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6.positive.wig_all.bw
track type=bigWig name="Plus brain D2" description="mRNA expression of whole brain in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2.negative.wig_all.bw
track type=bigWig name="Minus brain D2" description="mRNA expression of whole brain in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2.positive.wig_all.bw
track type=bigWig name="Plus brain F1" description="mRNA expression of whole brain in F1" visibility=hide color=0,0,200 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/F1.negative.wig_all.bw
track type=bigWig name="Minus brain F1" description="mRNA expression of whole brain in F1" visibility=hide color=0,0,200 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/F1.positive.wig_all.bw

whole brain

track type=bigWig name="B6 Positive" description="mRNA expression of whole brain in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6.negative.wig_all.bw

track type=bigWig name="B6 Negative" description="mRNA expression of whole brain in B6" visibility=full color=255,0,0 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/B6.positive.wig_all.bw

track type=bigWig name="D2 Positive" description="mRNA expression of whole brain in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2.negative.wig_all.bw

track type=bigWig name="D2 Negative" description="mRNA expression of whole brain in D2" visibility=full color=0,100,100 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/D2.positive.wig_all.bw

track type=bigWig name="F1 Positive" description="mRNA expression of whole brain in F1" visibility=hide color=0,0,200 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/F1.negative.wig_all.bw

track type=bigWig name="F1 Negative" description="mRNA expression of whole brain in F1" visibility=hide color=0,0,200 altColor=0,0,0 yLineMark=4 yLineOnOff=on priority=10 maxHeightPixels=256:256:64 autoScale=off yLineMark=4 viewLimits=2:10 yLineOnOff=on gridDefault=on bigDataUrl=ftp://tyche.uthsc.edu/user/xusheng/F1.positive.wig_all.bw

Help for bigwig

http://genome.ucsc.edu/goldenPath/help/wiggle.html