nanoporetech
Zero reads in index error
Good day, I am trying to detect base modifications but I keep getting a specific error. I basecalled using the Promethion instrument and got multiple bam files.
I then merged these bam files using the following command: samtools merge merged.bam *.bam
I then proceeded to sort and index the final file. From there I used the following command: modkit pileup Final.bam pileup.bed --log-filepath pileup.log I however get this error: calculated chunk size: 6, interval size 100000, processing 600000 positions concurrently attempting to sample 10042 reads Error! zero reads found in bam index
Could I please get some assistance on how to solve this? Thank you
Hello @setshabaTaukobong,
Did you run alignment concurrently with basecalling? To run modkit pileup you need to have reads aligned to a reference. You can inspect the base modifications on a read level with modkit extract and modkit summary.
Hi @ArtRand thank you so much for getting back to me. So just so understand, I would have to provide the sequencing machine with a reference file during basecalling?
Hello @setshabaTaukobong,
You can perform alignment during basecalling by providing a reference, or if you've already basecalled the reads I would align them to the reference using dorado aligner. I would not re-basecall the reads if you don't have to - just align them. Unless, of course, you want to use a different basecalling or modified base model.
