NMt2feat

We can then run NMt2feat as follows:

• TSS (--start)

  $NMt2feat -i S2/BY_S288c/BY_S288c_nuc.db \
            -o S2/BY_S288c/Features/Transcript/TSS \
            -f Data/BY_S288c/Features/features.gff \
            -l S2/BY_S288c/Features/Transcript/feature_id.txt \
            -w 500 -n 50 --start
  

• TES (--end)

  $NMt2feat -i S2/BY_S288c/BY_S288c_nuc.db \
            -o S2/BY_S288c/Features/Transcript/TES \
            -f Data/BY_S288c/Features/features.gff \
            -l S2/BY_S288c/Features/Transcript/feature_id.txt \
            -w 500 -n 50 --end
  

where -w 500 -n 50 indicates to NMt2feat that we want to consider 500bp from either side of the feature boundary and that we want to split these 500bp into 50 bins of equal sizes (i.e here 10bp). As you can see, the program NMt2feat creates a file suffixed by _avg.txt which is organized as a table with 6 columns separated by a single whitespace. Let's have a look at this table for the TSS:

$head -10 S2/BY_S288c/Features/Transcript/TSS_avg.txt
start 0 -500 -490 9330.19 11026
start 1 -490 -480 9296.27 11079
start 2 -480 -470 10313.1 12316
start 3 -470 -460 9256.08 11084
start 4 -460 -450 10371.6 12320
start 5 -450 -440 9372.42 11092
start 6 -440 -430 10484.1 12331
start 7 -430 -420 9491.17 11098
start 8 -420 -410 10593.3 12333
start 9 -410 -400 9552.06 11102

The columns indicate:

1. the interrogated feature boundary (here start=TSS),
2. the bin index (here from 0 to 99),
3. the starting position of the bin,
4. the ending position of the bin,
5. the total amount of signal into that bin,
6. the total number of probes falling into that bin.

Using the function NMt2featplot of the R pcackage, we can easily plot the content of the _avg.txt file. An exemple for the TSS is depicted in Figure 3.

Figure: