Gabriel Renaud
Gabriel Renaud
great, but beware that contDeam only gives you a ballpark estimate and there are a lot of assumptions in there. the iterative approach is the way to go :-)
I am currently on paternity leave and cannot do a lot of heavy work. Could you try running this on a cluster for the time being?
Hello! Just to be sure, did you realign everything to the MT or did you just isolate the mt reads from a bigger BAM file aligned against the genome? On...
ah! that is the issue, there are 2 ways forward: 1) manually hack the header to eliminate all the other references and reconvert to bam. I do not recommend this....
Dear Maria, I am teaching today and tomorrow essentially all day, just to acknowledge receipt of your issue. In the meantime, could you post the bam file somewhere and email...
I have a bit more time now, could you send me the full output from the console and ideally, send me the bam file via email if possible.
Hello! I think with calmd, it should be slightly larger as you add information, I would be worried about the intial value of 0.0, are you sture you have some...
thank you for the question! There is a possibility of bypassing the initial estimate and supply schmutzi with an estimate. However, be careful, then there is no way of teasing...
Hello! can you try running the script in R yourself? This could be a missing library issue.
> Having this implemented would be game changing!! I agree, I think Gaurav was having trouble getting the order of the reads right.