First row of RASQUAL output

natsuhiko / rasqual

Robust Allele Specific Quantification and quality controL

37 stars 20 forks source link

First row of RASQUAL output #46

Closed adamturner1 closed 3 years ago

adamturner1 commented 3 years ago

Hi Natsuhiko,

RASQUAL has been helpful so far for caQTL analysis and ATAC-seq data. It seems to be working when I use a wrapper script to run RASQUAL on all peaks in our dataset. However, I get 1.000000, 1.000000, etc. all across the first row of each output file (I attached a picture of what I get). The rest of the output all looks correct according to the Output section in the tutorial. I've tried a lot of things but always get this in the output.

rasqual_output

Do you think is due to some memory issue or something else? Also I assume this would not affect our results?

Any help would be much appreciated.

Thank you! Adam

natsuhiko commented 3 years ago

Hi Adam,

Could you also paste the command you typed here?

Best regards, Natsuhiko

adamturner1 commented 3 years ago

Hi Natsuhiko,

I use a wrapper script as follows:

The rasqual command I use is:

Apologies if this is a lot of lines. I used rasqualTools to prepare the input files. The 'exon_start_positions' and 'exon_end_positions' correspond to the start and end of each ATAC-seq peak. If I run RASQUAL on a feature (ATAC-seq peak) individually I don't get this error. Since I have thousands of ATAC-seq peaks I have to use the above commands but unfortunately keep on getting 1.000000, 1.000000, etc. and have not figured it out.

Thank you for your help!

Best regards, Adam

natsuhiko commented 3 years ago

Hi Adam,

If you remove -v option in the second last line of the above screen shot, what will happen?

Best regards, Natsuhiko

natsuhiko commented 3 years ago

Hi Adam,

I modified the verbose level so that you won't see this line with -v option. Sorry for the inconvenience.

Best regards, Natsuhiko

adamturner1 commented 3 years ago

Hi Natsuhiko,

Thank you for this!

Best, Adam