Questions tagged [long-reads]

Questions relating to long reads, such as pacbio or nanopore reads.

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Can multiplexing in Sequel II SMRTcells reduce the coverage?

I would like to have high depth of coverage of the transcriptome, but I need to analyze several tissues. I was suggested to pool all 5 tissue samples in same SMRT 8M cell. Will this result in a ...
  • 257
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somatic SNV tool for ONT samples

I'm looking for a tool to call somatic single nucleotide variations on reads from an Oxford Nanopore Technologies (ONT) run. I have both tumor and normal samples and have already aligned them to a ...
2 votes
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Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!

I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data. I have the file contigs.fa from short reads but phasing step with ...
  • 21
2 votes
1 answer

Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?

This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback on question format appreciated. I have ...