Robert Vaser
Robert Vaser
The FASTA file can be wrapped, i.e. the new lines are not the problem. Well, that depends on which version of racon are you using. Which is it? :)
Well, I have no idea then. Would you mind sharing the data with me via email so I can investigate further?
You can also try and check if `grep > reads.fasta | wc -l` equals half of `wc -l reads.fasta`.
Hello, can you check whether there is a read of length 0 in your FASTQ file or the file end is truncated? Sorry for the late response! Best regards, Robert
Hello Camilo, could you tell me which command generated `read_map.sam`? The error indicates that something is off with it. The reads and assembly file are alright. Best regards, Robert
Without option `-a` Minimap2 will produce a .paf file. Just run `mv read_map.sam read_map.paf` and run Racon with the new file.
Try using the original read file `all_m54163.subreads.fasta` or rerun Minimap2 with `trimmed_all_m54163.subreads.fastq`.
However you want :) If you want `.sam`, run Minimap2 with `-a`.
If you want a SAM file please run `minimap2 -t 64 -a consensus.fasta ${reads} > illumina.sam` (note the **-a**).
Hi, can you please elaborate on "resolve overlaps"? Best regards, Robert