Best Alignment Software that Integrates with Circos

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Britney Shepherd

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Mar 28, 2021, 3:53:55 PMMar 28
to Circos
Hello everyone!

I have just started my adventure with Circos and Bioinformatics for that matter, and I had some questions about alignment software and Circos. I am currently using Nanopore sequencing to generate a read from a sample. I used a software called EPI2ME (Which uses Minimap2) that showed which chromosomes the read from my sample were aligned to. I then ran an alignment against the specific chromosomes and my read using BBMap to find the best alignment sites and to generate a SAM file. 

Now to Circos... 

 I am trying to create a histogram mapped to Human Chromosomes 1, 2, 6, 9, 11, and 12 from the match data that was generated through BBMap (Called mhist in the command line arguments if you wanted to probe further). I have a decently general understanding of how to manipulate the config files to create an output, however I am encountering an issue where the data files that are generated from my alignment software are not compatible with the data files accepted by Circos. I guess my question is, is there any recommended software to generate alignment histograms/data where I can directly use that data as input to Circos? Or is there any way that I can use the data that was generated from BBMap directly to Circos?

I have attached the error from the command line when I pass the argument for my data, and if you want to view my config file to double check its not user error, please let me know!

Thank you in advance!Error.png


mostafa eltejaee

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Aug 3, 2021, 1:33:56 AMAug 3
to Circos
Hello,
As you see in error message, the syntax "chr start end value options" should be observed. Use MS Excel or google spreadsheet as the interface software to create proper input files for circos.

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