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Yes, cram has a great potential. It may ultimately replace BAM (if cram does not do that, there will be a binary format to achieve sooner or later). Nonetheless, cram may not replace BAM right now. It does not (at least did not) support all the tags. I do not know the progress on compressing unmapped reads. Furthermore, I am concerned with the compression model. I also think lossy compression is the way to go, but this should be done by reducing the resolution of quality, instead of by selectively dropping all the quality information.
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Originally posted by lh3 View PostYes, cram has a great potential. It may ultimately replace BAM (if cram does not do that, there will be a binary format to achieve sooner or later). Nonetheless, cram may not replace BAM right now. It does not (at least did not) support all the tags.
Originally posted by lh3 View PostI do not know the progress on compressing unmapped reads.
Originally posted by lh3 View PostFurthermore, I am concerned with the compression model. I also think lossy compression is the way to go, but this should be done by reducing the resolution of quality, instead of by selectively dropping all the quality information.
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I am the developer of CRAM and can answer any questions about it.
The code is here:
Reference-based compression of SRA data. Contribute to vadimzalunin/crammer development by creating an account on GitHub.
Documentation can be found here:
We just released v0.7, which is not a long term support yet but stable enough to try it out.
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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