Is There Any Public Available Raw Intensity Data From Rna-Seq

Question

[Zheng Chen]

Hi,

I am wondering if there is any public available raw intensity data from RNA-seq before the base calling. For my previous RNA-seq data analysis, I usually starts with fasta/fastq fomat, where I have information for each base and its quality score. Recently, I am investigating some model which makes use of the raw intensity data. If I understand it correctly, before base calling and after obtaining raw image data, there should be some intermediate steps where we can have the intensity/prob. distribution on each possible nucleotide on each base. I have googled related topics and found that ".bcl" files might be what I am looking for (please correct me if I am wrong), and I am wondering if there is any public available data as what I described.

Thanks!

Answer 1

[Ido Tamir]

This technote describes the real time analysis (RTA) basecalling. You find inputs and outputs there. "raw" intensity files are CIF. bcl files are intensities already converted to basecalls.

You should cooperate with some lab/sequencing institution to give you access to this data. I don't think there are recent public datasets available.