NMt2featcis

This program is an extension of NMt2feat which allows us to look at the entire cis-profile around a given genomic feature.

$NMt2featcis -i S2/BY_S288c/BY_S288c_nuc.db \
             -o S2/BY_S288c/Features/Transcript/txnuc \
             -f Data/BY_S288c/Features/features.gff \
             -l S2/BY_S288c/Features/Transcript/feature_id.txt \
             -u 500 -d 500 -p 50 -w 50 -s 10

Here we asked NMt2featcis to compute the cis-profile around all the transcripts annotated in BY genome by using a upstream and downstream region of 500bp (-u 500 -d 500) each divided into 50 bins of equal size (-p 50 -w 50) and by splitting the transcript region in 10 equal parts, whatever the size of the transcript region (-s 10). The program has created a file S2/BY_S288c/Features/Transcript/txnuc_cis.txt which is organized as a table with 9 columns separated by a single whitespace.

$head -10 S2/BY_S288c/Features/Transcript/txnuc_cis.txt
u 0 0 4710 0 10 10458.5 12350 4692
u 1 1 4710 10 20 9320.86 11108 4693
u 2 2 4710 20 30 10341.2 12352 4694
u 3 3 4710 30 40 9277.35 11113 4694
u 4 4 4710 40 50 10398.5 12356 4696
u 5 5 4710 50 60 9395.63 11121 4698
u 6 6 4710 60 70 10510.1 12364 4699
u 7 7 4710 70 80 9513.81 11125 4699
u 8 8 4710 80 90 10622.1 12366 4700
u 9 9 4710 90 100 9574.55 11129 4702

where the columns indicate:

1. the region:
   • u upstream the feature,
   • i inside the feature (here the transcribed region),
   • d downstream the feature,
2. the absolute bin index,
3. the relative bin index (w.r.t the region it belongs to),
4. the total number of interrogated features,
5. the starting position of the bin,
6. the ending position of the bin,
7. the total amount of signal into that bin,
8. the total number of probes falling into that bin,
9. the total number of features that contribute to that bin.

Finally, using the function NMt2featcisplot of the R pcackage, we can easily plot the content of the _cis.txt file. An exemple is depicted in Figure 4.

Figure: