Jared Simpson
Jared Simpson
Hi, The output files from call-methylation are zero-based, not 1-based. This is for compatibility with bisulfite sequencing data, which is usually in the 0-based bed format. The example bisulfite data...
Indeed, the end coordinates are encoded slightly differently. I will consider changing our end coordinate to match the BED output.
Hi, These errors indicate there are problems with the format of your fast5 files. Is this a relatively recent sequencing run? Jared
How old is the data? Could you email me a link where I can download an example fast5 file?
Thanks @oneillkza! We haven't trained a model for Q20 yet (or even tested nanopolish on it) but as it becomes more widely adopted we will. If you have tried it...
Hi @wangzhennan14, Sorry for the slow response, I was on holidays. Can you run grep the alignment record for that read (`cce11e44-9f88-45f8-8fa4-5fdf23314323`) and paste it here? Thanks, Jared
Hi @wangzhennan14, That link appears to be broken. Jared
Hi, This read is very long (>400kb), and some aligners may emit invalid CIGAR strings for such long reads. Can you let me know: 1. which aligner and version you...
Thanks. Can you send me the BAM record for this read? The SAM file looks ok but the CIGAR problem only happens in BAM. Jared
I don't think I ever received a bam file that allowed me to reproduce the problem, so haven't fixed it yet.