Example for RNAmotifs about rnamotifs

[Indigofera]

I have the same issue. I worked "Nova.txt" in "examples" directory. I got the same results: "NO significant tetramers". I checked the counting results. There are just some hit regions, mostly zeros.
Could you please check?

[matteocereda]

@xflicsu @Indigofera Hi guys, sorry for the delay. Just to let you know we are currently looking at your issue and we will be back to you asap during these days.
Thanks

[meettel]

Hi,
the problem was about the reference genome. There was a mistake in the README, where the reference genome was Human instead of Mouse. Now everything should work fine.
Watch out that in the manuscript we evaluated only degenerate tetramers containing R and Y.
Cheers,

Marco

[Indigofera]

Thanks for your reply.
I could not find this file "R/RNAmaps.R". Where is the file?

[Indigofera]

Sorry, previuos comment. You changed the file. I was looking the old one.

[meettel]

Exactly, it's "R/selection_of_tetramers.R" now.

[Indigofera]

thanks

[xflicsu]

@meettel , you changed the "RNAmotifs.sh" with as fellows:
##############################
TMP_FILE="tmp_${result_dir}.py"
echo "import m3_light" > $TMP_FILE
echo "m3_light.find_tetramers('${result_dir}', '${species}', '${half_window}','${min_height}','${percent_coverage}')" >> $TMP_FILE
python $TMP_FILE
rm $TMP_FILE
#####################
But I find the function "m3_light.find_tetramers" only deal with 3 parameters.
So, could you update this function?

Secondly, you only provide 5 parameters in readme when use "RNAmotifs.sh".
#######
./RNAmotifs.sh /absolute/path/to/RNAmotifs project_name splicing_change_filename.txt genome species
#######
But the input parameters of "RNAmotifs.sh" is 9.
Could you provide an example with 9 parameters?

BTW, I still can not get result like description as follows:

Selecting significantly enriched motifs...
[1] "NO significant tetrames"

[matteocereda]

Hi @xflicsu
we uploaded a .sh that will be available in the next upgrade of RNAmotifs, sorry for the incovenience.
We have now uploaded the original sh, things should work fine now.
Please use the correct genome (mouse for NOVA dataset).

[xflicsu]

Thanks! It works now.