scDNAseq data
Hello everyone, I am new here and totally new to the world of bioinformatics! In the lab we just got data from scDNAseq analysis (from a 384well plate, split in two for two different cell lines murine). I got different files: BAM, BIM, and fastq files... we are interested in getting info on the CNV in our cell lines, to know their aneuploid status. I tried alone to analyze them without any result. I don't know how to retrieve info from single wells, and to plot this data... I am really desperate as is a totally new topic for me, so any help would be greatly appreciate :) Thanks in advance!
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baldinifrancesca92 •
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What have you tried, what errors/issues are you facing, what platform/kit are you using, etc? This isn't really enough info for anyone to help.
Thanks a lot! Yeah I imagine, I am sorry I am not bioinformatician so I don't know basically anything! I really dont know where to start. I am using R studio to try to analyze the data. The data were provided by a scDNAseq facility called singlecellcore. I was trying to use aneufinder tool but I do not have the base and dont know where to start...
Still trying to understand what you mean by
scDNAseq. Was there a single cell per well of the plate that you refer to above or a number of cells?Did the facility tell you what technology/kit was used for the sequencing? That would be important information to know. I may have missed the advance that allows true single cell DNA sequencing without any amplification etc.
Thanks for the help! So, yes i have a single cells per well of the 384 well plate! Unfortuately the facility did not mention..they just provided pre-analysed data so the BAM file, with alignment to the reference genome. That's what they told me only....
Without specific details it is difficult to provide guidance. Someone else may be along with specific answers but in the mean time you can take a look at following.
https://bioconductor.org/packages/3.20/bioc/html/AneuFinder.html (this package now appears to be deprecated from bioconductor)
hhttps://github.com/rujinwang/SCOPE
https://github.com/raphael-group/chisel
If you have never done analysis with NGS data (and are not familiar with unix command line) then it may be best to ask for local help.