SG-NEx paper now in Nature Methods and Data Release Announcement

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Dear SG-NEx Data Users,

We are excited to announce the good news that SG-NEx manuscript is now out in Nature Methods! In comparison with bioRxiv preprint, this new version now includes:

• A detailed investigation and comparison of major isoforms identified by long-read and short read RNA-Seq
• Extended data resources, now including the new RNA004 sample
• Experimental validation of novel transcripts, fusion transcripts, and transcript expression for major isoforms identified by short and long read RNA-Seq data

You can find the open access paper here: https://doi.org/10.1038/s41592-025-02623-4

Additionally, we have updated the SG-NEx data release:

• Fastq files for all Nanopore long-read samples have been reprocessed using Guppy v6.4.2, which provides significant improvements over previous versions
• Reads have been realigned based on the updated fastq files, with Minimap2-2.22

For detailed information on the fastq and bam file updates, please refer to the release notes here: https://github.com/GoekeLab/sg-nex-data/tree/master

Thank you for your continued support! We value your feedback and welcome contributions in the form of tutorials or other resources.

Warm regards,
SG-NEx team