Hi, I am running into what looks like a similar issue as in #24 , but I am not sure if this is very related. Some important context is that I am trying to convert an aligned bam file output from the spaceranger count (version 3.0.1) pipeline using this dataset. My goal is to get a transcript-level alignment for this dataset, which I do not believe is provided by design in the spaceranger count pipeline, as it aligns reads to the transcriptome positions using STAR but uses a probe set reference which map to genes, not transcripts, in the final alignment. As such, I downloaded what I believe to be the exact reference transcriptome files used in the transcriptome I ran 10x's pipeline with.
Soon afterwards, I came across this repository, which seems like a promising alternative to the old sam-xlate tool which I have not been able to successfully get running. I am able to successfully download and install mudskipper with no issues, but I am not able to make the conversion step happen. I am able to construct an index from my .gtf file, but after doing so I get the following error:
$ RUST_BACKTRACE=debug mudskipper sc --index mudskipper_index/ --alignment possorted_genome_bam.bam --out mudskipper_modulated.bam
[2024-07-05T23:01:35Z INFO mudskipper] Mudskipper started...
thread 'main' panicked at src/main.rs:241:62:
called `Option::unwrap()` on a `None` value
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::panicking::panic
3: core::option::unwrap_failed
4: mudskipper::main
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
I also ran it directly on my .gtf file directly with a full backtrace from rust, which produces the same error:
Hi, I am running into what looks like a similar issue as in #24 , but I am not sure if this is very related. Some important context is that I am trying to convert an aligned bam file output from the
spaceranger count(version 3.0.1) pipeline using this dataset. My goal is to get a transcript-level alignment for this dataset, which I do not believe is provided by design in thespaceranger countpipeline, as it aligns reads to the transcriptome positions using STAR but uses a probe set reference which map to genes, not transcripts, in the final alignment. As such, I downloaded what I believe to be the exact reference transcriptome files used in the transcriptome I ran 10x's pipeline with.Soon afterwards, I came across this repository, which seems like a promising alternative to the old
sam-xlatetool which I have not been able to successfully get running. I am able to successfully download and installmudskipperwith no issues, but I am not able to make the conversion step happen. I am able to construct an index from my.gtffile, but after doing so I get the following error:I also ran it directly on my
.gtffile directly with a full backtrace from rust, which produces the same error:Any assistance with this issue would be greatly appreciated. Here are some details of my setup (Ubuntu 22.04) in case these will be of any help: