Hey Nicole,
I am trying to find 2.9 upgrade from GS Jr, but cannot. Can you please point me in right direction?
-
Hello Krisztab,
This is a feature built into software version 2.9. When processing long amplicons on the GS FLX+ platform, there are three signal processing options offering varying degrees of read filtering stringency. The first pipeline is the most similar to the current Amplicon pipeline, which is the most stringent and rejects reads of poorer quality. The other two pipelines are more similar to the shotgun pipeline and will trim back the poorer quality bases from reads rather than reject the entire read. These pipelines will also reject reads trimmed shorter than 700 flows (~390 base pairs) which can be recovered by changing the qualityMinLength filter and reprocessing or reprocessing with the shotgun pipeline.
You may want to ask your sequencing provider to reprocess with the other pipelines to determine which is best suited for your needs.
Regards,
Nicole
Nicole Whitney
Senior Specialist
Customer Support
454 Life Sciences, A Roche CompanyLeave a comment:
-
Roche FLX+ software update v. 2.9
Hi there,
Roche released a new version of its software for FLX+, you can read the announcement here:
http://www.roche.com/media/media_rel...2013-08-06.htm
"The latest software enables sequencing of amplicons up to 800 bp while maintaining >99% accuracy over the length of the read."
The sequencing company I use already tests this software, and they have sent me the results processed with the new version. I got fewer sequences, which is due to the fact that there are no sequences shorter than about 365 bp. So of course this results in higher average sequence length.
Does anyone know if this cutoff is a built-in feature of the new version, or just something you can implement if you want?
-
The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i
...01-24-2023, 01:19 PM -
Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.
The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes...01-09-2023, 03:10 PM
Leave a comment: