Robert Vaser
Robert Vaser
Hi Michal, the mentioned approach should work but I haven't tried it myself. Best regards, Robert
Hi Thierry, sorry for my late reply, try using option `-u` to see whether you will get anything (it should print out unpolished contigs). You can also paste here the...
The problem is that only the second and last read have an alignment with the backbone. The last read has the same name as the backbone so it is not...
Hello, which version of racon are you using? Best regards, Robert
It is really strange that this particular error occurs. Would you mind sharing your data so I can investigate further? Best regards, Robert
How large is the created sam file and how much RAM does your machine have?
Could you please add the following lines of code at https://github.com/isovic/racon/blob/master/src/polisher.cpp#L330: ```cpp for (uint64_t i = 0; i < overlaps.size(); ++i) { if (overlaps[i] == nullptr) { fprintf(stderr, "Null at...
Sure, send me the error you are getting when building from source.
The error means that the read identifiers weren't replaced with read IDs in overlaps, see here https://github.com/isovic/racon/blob/master/src/overlap.cpp#L129-L177. I don't know how this output is even possible, if a overlap isn't...
Can you please paste here a couple of non-header lines of your SAM file, and a few sequence headers from Illumina reads and polished contigs?