Downloading Data failure and QV calculation

[Yoon90]

I've tried to download your corrected data via:
wget http://complex.zesoi.fer.hr/data/downloads/HG002.experimentalUL.corrected.fasta.gz
But it doesn't seem like work and i could not download the data. Could you check the link again?

And one more thing, How did you calculated the QV of corrected reads? - as far as i know the output format of corrected reads is .fasta which does not have QV. I'm sorry if i'm wrong about this.

[dehui333]

Hi,

Please try again with the following:
wget -O HG002.experimentalUL.corrected.fasta.gz https://zenodo.org/records/13252378/files/HG002.experimentalUL.corrected.fasta.gz?download=1

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Regarding QV,

The corrected reads themselves do not carry information about their quality.

We obtained some form of measurement of the quality of reads via two ways:

1. Aligning the reads to a high quality assembly of the same sample (if one exists) and measure the agreement between these reads and the aligned-to segment (e.g. using bamConcordance (https://github.com/PacificBiosciences/hg002-ccs/blob/master/concordance/bamConcordance) to get some form of Phred-scaled score, or just calculate accuracy from the CIGAR string).
2. Using yak (https://github.com/lh3/yak) to obtain a QV using illumina short reads from the same sample.

Best,
Dehui