SchulzLab

Hi Dario, can you please post the call with the oases pipeline script here, this seems odd. Just out of curiosity how much memory is available on the machine where...

Dear Dario, I was wondering if you had some unusual flags set during compilation. For example the -LONGSEQUENCES, BIGASSEMBLY flags should be turned of , but that is the case...

Hi Dario, I don't think it has to do with the C version. I would suggest to use read normalization. Regards, Marcel

Hi Katherine, velvet accepts this interleaved paired-end format as mentioned in the documentation (see here https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf). It should work fine you don't need to split up into 2 files. Hope...

About the question why higher kmer values take too much RAM. The higher k, the larger the number of unique kmers that form unique nodes in the graph. At higher...

Hi, can you try to edit the Oases makefile and also set export MAXKMERLENGTH = 127 This should work. Hope that helps, Marcel

Hi, sorry for my delayed response, but I was traveling the last weeks. If I understand correctly Oases is able to assemble the dataset with kmer value 19 and 21...

Hi, we are still not sure what the problem is. Is there anything particular with the one sample were you get the error McGlock? Kind regards, Marcel

Dear Xia Han, this is a problem with DSK. I found an issue in their GitHub were this was fixed: https://github.com/rundsk/dsk/issues/105 We will look into how to update this as...

Hi, I get exactly the same problem with the normal pipeline not using the --rrbs flag. Once I run (see command lines below) the bs3-align.py it returns only: BS-Seeker3 beta...