Simon Heath

Hi Andy, The format for the dbSNP index has changed a lot in recent releases of gemBS. Was the index created with the same version of gemBS that you are...

Hi Andy, If you use the underlying tools (bs_call, mextr and snpxtr for the calling, methylation and SNP extraction) there are options for restricting operations to a list of regions....

You need the --contig-bed option - you can supply a bed file with regions and just those regions will be called. Simon On Sat, Mar 21, 2020 at 1:05 AM...

Hi Paul, Our cluster has a Lustre FS for bulk storage and a small shared NFS filesystem for home directories. I tend to run gemBS from the NFS filesystem, but...

Hi, It shouldn’t take this long - at what stage in the pipeline are you ? Simon > On 3 Sep 2019, at 04:21, YingYa wrote: > > Hello lrsantiago,...

Hi Leandro, What aligner are you using? bs_call should be able to work with BAMs from novoalign, bwameth, bismark, bsmap and gem3 (with the appropriate flags for BS processing where...

Is there any chance that you could provide me with the input files you used when you tried to run bs_call by hand with hg38? How much memory do you...

Dear Bekir, Thank you for the report. Would you have a set of these reads that you could share with us? The mapper should only soft-clip if there are mismatches...

Dear Bekir, Can you tell me the version of gemBS that you are using and the analysis parameters? Thanks, Simon > On 27 Jul 2018, at 11:33, berguner wrote: >...

OK thanks - that should have worked. I’ll look into it. Simon > On 30 Jul 2018, at 10:05, berguner wrote: > > Dear Simon, > > I was running...