gappedPeak not working

[NMaziak]

Hello,

Thanks for providing a wonderful tool! I have pyGenomeTracks version 3.8. I have a gappedPeak file, the first two lines look like this:

chrY    887530  917120  Peak_7  .       .       887570  887820  255,0,0 3       1,250,1 0,40,29589      294.0   -1      -1
chrY    925470  955780  Peak_12 .       .       931520  933260  255,0,0 3       1,1740,1        0,6050,30309    77.0    -1      -1

However, when I plot it, it comes out looking like a normal peak, in the .ini file, I have the following:

[HMMRATAC]
file = ATAC_bw/sample_peaks.gappedPeak
file_type = bed

Would you happen to know why it won't work?

Any help is greatly appreciated.

Best, Noura

[lldelisle]

Hi, Do you have tabulations in your file? Do you have an error message? Thanks, Lucille

[lldelisle]

I will have a closer look tomorrow.

[lldelisle]

It seems that your 'gappedPeak' does not follow exactly the format described by UCSC: https://genome.ucsc.edu/FAQ/FAQformat.html#format14 And this is what pyGenomeTracks gives as message:

Warning: The block field 5 (score) is not valid: ..
Error message: could not convert string to float: '.'
Only the first 4 fields will be used.

There are 2 ways to convert your gappedPeak file to a 'conform' gappedPeak file:

• With awk: awk -v OFS="\t" '{$5=0;print}' input.gappedPeak > fixed.gappedPeak
• With sed: sed 's/\.\t\./0\t./' input.gappedPeak > fixed.gappedPeak

Here is the result:

Feel free to reopen the issue if the error is still here.

[NMaziak]

Hi Lucille, thank you so much for the prompt reply. I didn't catch the warning, very sorry about that. Will fix it!