Robert Vaser
Robert Vaser
Yeah, It should be a fastq file. Did you by any chance mess up the indentation in the script?
There you go. [rename.zip](https://github.com/isovic/racon/files/3218310/rename.zip)
If you have a big file it might take a while :)
Indeed it is. I hope you run the command with piping to a new file!
`python rename.py 98ZLc_combineraw_IL.fastq > 98ZLc_renamed_IL.fastq`
Unfortunately yes.
Hello, it appears that you passed the wrong path of the `SAM` file to Racon. Best regards, Robert
Hi Michal, the wrapper problem is probably in the path of rampler when using bioconda (and possibly racon). I'll have to fix this but for the moment you can compile...
Hello, are the 3 missing contigs small? Sometimes due to lack of coverage some smaller contigs drop out after polishing, but you can retain them with option `-u` (`--include-unpolished`). Which...
Can you please copy the commands you used in running Racon with Illumina data (both mapping and Racon step)?