The reported position of identified motif in the occurrence file does not seem to be accurate

[yasamanrezvani]

Hello,

Thank you for the fantastic tool that you have provided to perform the denovo motif search.

I think I have found a bug in the .occurence file outputted from the denovo motif search. According to the documentation, this file should contain the coordinates of the identified motif relative to the coordinate of the input sequence (the column is called start..end). However, the location does not seem to report the right position of the motif hit.

For example, the first line of the following screenshot demonstrates that the start of the pattern position is 1303 bp from the beginning of the sequence (3756384) however if I add up these two numbers, I get a number larger than the length of the sequence. I am unsure if the numbers are precisely reported or if I am missing something here!

[wge11]

Hi @yasamanrezvani,

thanks for your report.

The start and end possition here indicate pseudo-coordinates here. The tool first append the (-) strand in a reverse complementary manner to the (+) strand, seprated by a letter N, i.e. [+strand sequence]N[-strand sequence], and then scan the sequence for motifs. Thus in your case, the motif is found on the - strand, which is 459 bp (2x885-1311) to 467 bp (2x885-1303) away from the sequence start position (3756384).

Hope it helps with interpreting your results.

Best, Wanwan

[yasamanrezvani]

Hi Wanman,

Thank you so much for replying back to me!

Could you please give an example of a negative-strand as well? It will be 2 cases if the motif is found on the negative strand sequence or the complementary strand. Just need to make sure I understand the logic.

I appreciate your help!