Open sumin5784 opened 3 years ago
What I usually do is basecall the data again with --fast5 out option during basecall. That way I have the fast5s with sequence information already in it. Then, I convert these fast5s into single fast5s and then proceed with resquiggle command.
What I usually do is basecall the data again with --fast5 out option during basecall. That way I have the fast5s with sequence information already in it. Then, I convert these fast5s into single fast5s and then proceed with resquiggle command.
Not possible with guppy.
It is possible on guppy but use an earlier version ( I would recommend any version before 6.3) of it as --fast5_out flag was deprecated in the recent versions.
I would recommend converting to Remora for raw signal alignment which uses standard POD5 and BAM files as input, greatly simplifying these issues.
Hello,
I did resquiggling and got errors, so was trying to annotate raw files with fastqs. And I'm keep having weird results from annotating. I tried two times but tombo can read all the fast5 identifies, but nothing is annotated. I'm using published dataset, so not sure whether the file has problems or not. I downloaded data from NCBI SRA, and fast5 files are single-fast5 files, but I only have one fastq file, which I fetched out using fastq-dump in SRA Toolkit.
If fastq file has problems, then what can I do next? Do I need to do basecalling on my own? Could anyone give me feedbacks?
Regards, Sumin