pbfusion

[tky199996]

Hello, when I run pbfusion's sample file, pbfusion gff-cache --gtf gencode.v38.annotation.gtf, it works fine. But when I want to run the Gal6a version of the gtf file, the following error occurs: thread 'main' panicked at 'Missing feature annotation 'gene_name'', src/annotation.rs:468:28 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace What went wrong and how do I fix it?

[tky199996]

您好，当我运行 pbfusion 的示例文件 pbfusion gff-cache --gtf gencode.v38.annotation.gtf 时，它工作正常。但是当我想运行 gtf 文件的 Gal6a 版本时，会出现以下错误： thread 'main'paniced at 'Missing feature comment 'gene_name'', src/annotation.rs:468:28 note: run RUST_BACKTRACE=1withenvironment variable to显示回溯 出了什么问题以及如何修复它？ My gtf file is a comment file about the gal6a version of Red Jungle Fowl

[zeeev]

Hi @tky199996 ,

Check if the GTF contains features that are lacking a gene_name field. Pbfusion requires that each feature contain a gene name. You can remove those entries and it should work.

[tky199996]

你好@tky199996,

检查 GTF 是否包含缺少gene_name 字段的功能。Pbfusion 要求每个特征都包含一个基因名称。您可以删除这些条目，它应该可以工作。

Thank you for your quick reply, in fact I don't understand how to check, my gtf file is the reference genome of red jungle fowl downloaded from ensembl without any modifications, can you tell me what should I do? Thank you again

[tky199996]

你好@tky199996,

检查 GTF 是否包含缺少gene_name 字段的功能。Pbfusion 要求每个特征都包含一个基因名称。您可以删除这些条目，它应该可以工作。 Thanks, I got it, I will try and do it again, thank you very much

[tky199996]

你好@tky199996, 检查 GTF 是否包含缺少gene_name 字段的功能。Pbfusion 要求每个特征都包含一个基因名称。您可以删除这些条目，它应该可以工作。

Thank you for your quick reply. I downloaded the visual py script in your repository locally. When running the script using python3, the following error occurred. What went wrong?

[zeeev]

Can you send a few hundred lines of the GTF file so I can take a look? The error is telling me that there's a missing field called "gene_name", you can probably just add that entry, by coping ID or some other unique identifier.

[tky199996]

Can you send a few hundred lines of the GTF file so I can take a look? The error is telling me that there's a missing field called "gene_name", you can probably just add that entry, by coping ID or some other unique identifier.

Hello, I deleted the gtf file that lacked 'gene name' according to the method you mentioned before. I can run pbfusion gff-cache normally, but an error occurred when using the script for visualization. Traceback (most recent call last): File "/home/tianky/full-length-transcript/FL_denovo20230616/33.rna_classification/33.heart/funsion/visualize_fusion.py", line 231, in main(args) File "/home/tianky/full-length-transcript/FL_denovo20230616/33.rna_classification/33.heart/funsion/visualize_fusion.py", line 227, in main plot_fusion(ref_genes, alignments, breakpoints, args.output) File "/home/tianky/full-length-transcript/FL_denovo20230616/33.rna_classification/33.heart/funsion/visualize_fusion.py", line 128, in plot_fusion gene1_start = min([x[0][1][0][0] for x in list(alignments.values()) if x[0][0] == breakpoints[0][0]]) ValueError: min() arg is an empty sequence

[tky199996]

Can you send a few hundred lines of the GTF file so I can take a look? The error is telling me that there's a missing field called "gene_name", you can probably just add that entry, by coping ID or some other unique identifier. Hello, this is my bam file after alignment using pbmm2. Do I need to delete the first few lines?

[zeeev]

Hi @tky199996,

I'm going to close out this issue. I see you were able to run pbufsion successfully. There is a ticket open for the other issue you described: https://github.com/PacificBiosciences/pbbioconda/issues/660

Did you find any biologically meaningful fusion genes?

[tky199996]

你好@tky199996,

我要结束这个问题了。我看到您能够成功运行 pbufsion。您描述的其他问题有一张票：#660

您是否发现了任何具有生物学意义的融合基因？ Hello, I have found the fusion gene and just want to visualize it. I wonder if you have fixed the visualization problem? If you release a new version, I hope to try to visualize the fusion gene. Thank you for your help. At least I have found the fusion gene. Your software has helped me a lot. Thank you again.

[zeeev]

Can you please post your comments to this thread, where we're addressing the issue: https://github.com/PacificBiosciences/pbbioconda/issues/660