Peak-motif option to avoid purging

[jvanheld]

With Znf362, we notice that the positional profiles of nucleotides show a strong valley in the center, for all the nucleotides. The same holds for all dinucleotides.

This results from the purge-sequence step, which masks repeated elements with Ns. The motifs discovered in these peaks are all AT-rich low complexity motifs;

To test : add an option -no_purgeto peak-motifs and check if

• more informative motifs appear
• the benchmark scores in the leaderboard tests are improved

[jvanheld]

I added the option -nopurge to peak-motifs

This indeed completely changes the shape of the nucleotide positional distribution profiles.

The effect is also very clear on dinucleotide compositions.

With purged sequences

Strong depletion in the middle for all dinucleotides

With the option -nopurge

Peak of AA and TT in the middle, but no peak for AT, this is thus not a simple enrichment in A+T

[jvanheld]

The motifs discovered with peak-motifs are completely different depending on whether the option '-nopurge' is activated or not.

Motifs discovered on purged peaks

Analysis: IBIS24_leaderboard_ZNF362_THC_0364.Rep-DIANA_0293 (28/06/2024 13:26)

Motifs discovered on unpurged peaks

Analysis: IBIS24_leaderboard_ZNF362_THC_0364.Rep-DIANA_0293 (06/07/2024 11:51)

[jvanheld]

@brunocontrerasmoreira and @najlaksouri

Interesting to see the differences between motifs discovered with / without purging the peak sequences in this particular peakset. I wonder if we will see so drastic differences with other peaksets as well.