Mon, 11/25/2013
Customer is a yeast biologist, and he wants us to help determine break-point locations in pair-ended sequences.
Mon, 11/25/2013 at 4:42 PM
AccuraScience LB: Is it going to be DNA sequences or RNA sequences for which breakpoint locations are to be determined? Is this for determining chromatin rearrangement or gene fusion events?
Tue, 11/26/2013 at 9:27 AM
Customer: These are gene fusions, and we will have budding yeast paired-end DNA reads.
Tue, 11/26/2013 at 11:07 AM
AccuraScience LB: Could you provide more details about the project and about the data (e.g., how many samples, how many reads, read lengths)?
Wed, 12/11/2013 at 10:34 AM
Customer: We have about 200 genomes of Saccharomyces cerevisiae containing rearrangements, 200 base paired-end reads at about 50x read depth. We need to find breakpoints in the genomes.
Wed, 12/11/2013 at 4:36 PM
AccuraScience LB: Our pipeline for analyzing this dataset would include the following steps: 1) raw data quality control; 2) breakpoints detection using fusionmap, 3) data visualization by ciscos plot.
There is some uncertainty as of whether fusionmap will work well, because this tool was not developed for yeast genome. In case it fails, we would develop a customized strategy to replace step 2), and this strategy would include the following steps: i) Initial mapping of all reads to the reference genome; ii) Re-mapping unmapped reads; iii) Candidates breakpoints searching, based on the read-level data from ii); iv) Refine the candidate breakpoints taking all relevant evidence into account.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer’s privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.