Litt
Litt
Okay, so there was a smaller truncated pod5 written by the device (a software crash occurred during this run) that I included in the above sample data. I thought maybe...
@ollenordesjo The first offending line doesn't have a None at the end and does have a '_1' in the readname - does that one have anything else that looks fishy...
@ollenordesjo I pulled the line of the unsplit read from the mapped SAM file (the one I generated before realizing there were a lot of concatenated reads): 125659e2-2885-4568-b285-f3304db0097e 16 chr4...
@ollenordesjo how do I remove this data?
@ollenordesjo also how are other people getting good results without doing this if the start/end comment is automatically written? Noah
@ollenordesjo okay thanks i'll try that. Also the only other flag I'm using with minimap2 is -Y, so that everything is soft clipped (no hard clipping). Makes it easier for...
@ollenordesjo the sed command did not work though - same error. Edit: I ran split with the non-modified-basecalling files output during the original run and everything converted to BAM fine....
@ollenordesjo could my Samtools version be an issue?
@ollenordesjo It's all good! I'm using Samtools version 1.16.1 and htslib 1.16, which are from 2022 so pretty recent. How would I give you access to the SAM? It's like...
@ollenordesjo it's saying undeliverable to that address