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Data from the sequencing of the whole genome with LOW quality.

Hi! I am looking for large NGS Runs (more than 50GB for Run) with low/medium quality, which need additional quality control by applications like trimmomatic. Could someone advise me some experiment/runs like SRR988073 (preferred whole genome sequencing), but much larger?

next-gen sra sequencing genome quality
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updated by jotan jotan • written by mieszko91 • mieszko91

2 answers

You can search the NCBI-SRA database for the larger data sets. But the quality info can only be retrieved if they report it in the related publication. Are you looking for data with adapter containg reads or the low phred quality score? You can check the recent Aegilops taushii, Triticum urartu or the hexaploid wheat.I am not sure about the quality stats for these data.

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written by Shyam Shyam

Hi!. Thanks for your answer. I am looking for reads with low phred quality and they also may contain adapters

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written by mieszko91 • mieszko91

I dont think I can help you there. As far as I now, very little percentage of reads contain adapter and low quality reads. Can't you simulate the data?

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written by Shyam Shyam

This paper might be a useful reference

Large-Scale Quality Analysis of Published ChIP-seq Data

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written by jotan jotan

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