Nadia Davidson

Hi Luyi, Thanks for FLAMES! We're been using the cell barcode matching code for fusion calling in long read single cell data (with JAFFAL) and I've noticed that some fusions...

Sorry for the VERY slow reply to this. I assume probably not relevant anymore, but I will answer for the sake of others with similar issues. JAFFAL (and JAFFA) perform...

Hi Huseyin, Sorry for the very slow reply to this message! I've only just seen it now. This looks like an issue related to bpipe, so I think your best...

Thanks Marek, we'll have a go on a small dataset and then chat with you more if it looks promising. No need to make a separate branch at this stage.

Hi, Running out of memory from one bam seems unlikely with 128G. Can you please send me some more details about the run such as version of corset, size of...

Hi, Thanks all for reporting this. There were some major changes to the data structures introduced into corset in version 1.08, so this may have introduced a bug as well....

Hi Domenico, Thanks for reporting this. I suspect our installation script is may not be installing Trinity plugin such as seqtk-trinity correctly. So I'll investigate. Just to confirm, did you...

Hi Domenico, Do you have an earlier version of gcc available, maybe 4 or 5? I think a lot of these problems are related to dependent packages not being compatible...

Hi , You need to specify the short reads paths, reads_R1 and reads_R2, in the contig file, so it can perform genome-guided assembly and count reads mapping to genes (even...

You could try dummy fastqs although I suspect completely empty files might cause a few errors in Necklace, so best to provide some real or simulated reads from the same...