Simon Heath

gemBS simply calls gem-indexer and there is nothing to stop you invoking this outside of gemBS. To find gem-indexer look in bin/ in the gemBS install directory (normally /usr/local/lib/gemBS or...

Hi Bekir, We would be quite happy to add this, but I need a bit more information. How would you propose that the prioritization should work - through resolving multimaps...

Hi Bekir, OK, I have some ideas on this and I will try them out with a few RRBS datasets. We can clearly add mapping statistics counting the number of...

It is one of the projects I am working on at the moment. I will reply to this thread when I have something to test. Simon > On 27 Mar...

If you have some testing datasets that would be great. It need not be an entire dataset - just 10 millions reads or so - and ideally one single end...

Not normally, unless you are expecting to see a large fraction of DNA fragments that are less than 1 read length. In general the GEM3 mapper is quite good at...

Hi Bekir, Thanks for the report. The libraries that we see mostly have many pairs where the two reads overlap, but very few where the insert size is less than...

Hi Bekir, In principle the new version of gemBS (3.0.0) should have this feature. The --keep-unmatched option to gemBS call will not discard read pairs that are not pairing correctly....

Would it be possible to get a (ideally small) FASTQ pair that shows this problem that you could share with me? Thanks, Simon On Thu, Nov 14, 2019 at 6:23...

Dear Diana, Would it be possible to get a small dataset that you could share that reliably causes this crash? Yours, Simon On Fri, Dec 2, 2022 at 12:37 AM...