Simon Heath

It’s difficult to see where to go from here. If you could create a example dataset that consistently failed (or at least failed with a reasonable frequency) that you could...

I will work on making the error messages more informative to try and make it simpler to track down problems such as those you highlighted. Simon > On 27 Aug...

The GPU version of gem3 is not methylation aware so cannot be used with gemBS. Simon On Wed, 17 Aug 2022, 21:02 Jake Lehle, ***@***.***> wrote: > Hmmm good question....

Hi Alex, There should be no major problem getting this working. The methylation part has a few changes w.r.t. the classic gem and I don't think it would be that...

No, I have to port the fix to the gembs branch. Simon On Wed, 15 Jun 2022, 22:06 Ismail Moghul, ***@***.***> wrote: > Thanks for getting to the bottom of...

Normally because the conversion control sequences haven't been correctly specified or for some reason not enough reads mapping to the conversion controls were found. Simon On Wed, 25 Mar 2020,...

Thanks for the report. The documentation for the bigbed format is very scarce and it is possible that some aspect of the summary data is not being produced in the...

Thanks, so it looks like I might just need to change the header. Simon On Thu, 18 Mar 2021, 20:56 Paul Sud, ***@***.***> wrote: > Just an update: we are...

It sounds like there may be a problem with the input FASTQ file. Is there a possibility that the read IDs are not unique? If a small dataset showing this...

Can you send a fragment of the BAM file from gem and from BSMap (with the same reads)? Simon On Wed, 25 Mar 2020, 19:45 Stefano Pirrò, wrote: > Dear...