There are some errors running bam file #51
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It seems the ASCAT failed to get results, you can run https://github.com/VanLoo-lab/ascat analysis (it has been maintained and updated) by your own and check this. |
Hello, could you kindly provide me with two test BAM files? I would like to determine whether the issue lies with my data or if there is a problem with the installation of my software. |
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I generated a debug path for testing the pipeline, please see https://github.com/ShixiangWang/gcap/tree/master/test-workflow/debug |
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You can refer to goole to see how to download data from SRA, it's quite easy. |
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Also, if you have multiple samples, you can use other sample to test the workflow. |
Hello, thank you very much for your help, I have solved the problem of the program. But now I have a guess, whether I can use inferCNV and other software to analyze the scRNA-seq, obtain the corresponding copy number data, and build a table similar to "ascn" for eccDNA prediction.Thank you very much for your help. |
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In logic, it makes sense, however, the single cell data cannot provide accurate absolute copy number profiles, so it will largely fails using gcap, as the copy number is a dominant predictive feature. I beleive there some ongoing developments for sc data, I once wanted to do a job similar to this, but have not been able to do so yet. You have to take a risk for using it, and you'd better add the necessary filtering and verification to the results. |
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Hello, I would like to ask, I want to use the data of cancer cell lines to run, and I need to pair normal samples, how should I choose this normal sample, such as the para-cancer data corresponding to cancer, the sequencing data corresponding to tissue, or the data of embryonic stem cells? Do you have any recommendations.Thanks. |
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For cancer cell line data, it would be better to use WGS. However, if you only got WES, just run the cnvkit to get absolute copy number values and use the integer copy number to infer the results (the accuracy should be lower). On the other hand, if you have your own samples, sequencing with Circle-seq is a good option. |
Thank you very much for your advice. My data is collected as WGS data, but I'm not sure which normal samples of cancer cell lines to use for comparison. For instance, now that I have obtained the data of the gastric cancer cell line, can I use the data of normal gastric tissue, normal gastric cell culture, or embryonic stem cells as its normal group data? Which data is more in line with practical theory? |
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For WGS data, you can use the AmpliconSuite, it uses tumor WGS as input, no normal control is required. |
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Hello, when I used AA for ecc recognition of WGS data, I found that the results obtained were very few, even 0, which was very difficult to analyze in bioinformatics. Do you have any good suggestions for using the software? Thank you very much.
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主题: Re: [ShixiangWang/gcap] There are some errors running bam file (Issue #51)
For WGS data, you can use the AmpliconSuite, it uses tumor WGS as input, no normal control is required.
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You can tune the parameters of AA. |
Hi,
I conducted a test on a dataset and generated my BAM and BAI files using 'samtools'. However, I encountered some errors during the process. I would appreciate any solutions you might have. Additionally, please let me know if there is anything I may have overlooked while executing the workflow."
Best,
Yang
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