GenomicTools: an open source platform for developing highthroughput analytics in genomics - Open Source Software in Life Science Research - page 201

$ head offset.txt
ENSMUSG00000090025:ENSMUST00000160944

$ head offset.txt
ENSMUSG00000090025:ENSMUST00000160944 0.007850
ENSMUSG00000090025:ENSMUST00000160944 0.007850
ENSMUSG00000090025:ENSMUST00000160944 0.021899
ENSMUSG00000090025:ENSMUST00000160944 0.021899
ENSMUSG00000090025:ENSMUST00000160944 0.030098
ENSMUSG00000090025:ENSMUST00000160944 0.030098
. . .

0.007850

ENSMUSG00000090025:ENSMUST00000160944 0.007850

ENSMUSG00000090025:ENSMUST00000160944 0.021899

ENSMUSG00000090025:ENSMUST00000160944 0.021899

ENSMUSG00000090025:ENSMUST00000160944 0.030098

ENSMUSG00000090025:ENSMUST00000160944 0.030098

...

Finally, the computed offsets can be separated in genes of high versus
low expression, histogrammed using the vectors tool (operation 'hist')
and plotted using R (see Figure 8.5 for a sample plot), Excel or any other
similar tool or environment. For example, if the 'offset.txt' fi le computed
above was separated into two fi les 'offset.high.txt' for the genes of high
expression and 'offset.low.txt' for the genes of low expression, then:

$ cat offset.high.txt vectors -hist -n 6 -b 100 > profi le.high.txt $ cat offset.high.txt vectors -hist -n 6 -b 100 > profi le.high.txt

$ cat offset.low.txt vectors -hist -n 6 -b 100 > profi le.low.txt $ cat offset.low.txt vectors -hist -n 6 -b 100 > profi le.low.txt

$ head offset.high.txt
#bin-start

$ head offset.high.txt
#bin-start bin-freq bin-freq bin-counts bin-counts

0.000000 0.000000 0.008555 0.008555 20676 20676

0.010000 0.010000 0.008522 0.008522 20596 20596

0.020000 0.020000 0.008128 0.008128 19644 19644

. . . . . .

￿ ￿ ￿ ￿ ￿

Example of TSS read profi le for genes of high
and low expression

Figure 8.5