tracer
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Teichlab
TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
Can't determine the origin of this error. As far as I know, Tracer is not trying to use the display variable. Also didn't see this error anywhere I could search...
Hello, I'm trying to build a running tracer on a more modern version of python (3.8.10). SInce then, Bio.Alphabet has been removed from python, and the recommendation is that calls...
…f Bio Alphabet dependencies in old pkl objects.
Thank you for developing tracer! I am currently trying to run the tracer docker container using singularity without success. If for example I run `docker run teichlab/tracer test` I get...
Hi, Setting the trinity_kmer_length option in the config file leads to this error from trinity: `ERROR, don't recognize parameter: --KMER_SIZE` Based on [this](https://groups.google.com/g/trinityrnaseq-users/c/XUxfT96zpds/m/a7QFeKbJBQAJ), I believe that `--KMER_SIZE` should be changed...
Hi, Similar to this issue https://github.com/Teichlab/bracer/issues/21#issuecomment-417711510 in BraCeR, can one run TraCeR on the per-cell fasta files demultiplexed from filtered_contig.fasta output of cellranger vdj? If yes, then with what adjustments?...
Hi, below is the KeyError error that I get with tracer assemble. It is only one out of 1536 samples, so otherwise the software is running very nicely. Below the...
Hello, I have a naive question about whether all VDJs have equal chance to be detected. How do you know whether there is any bias in covering the theoretical VDJ...
Hello, I seem to be having an issue with the IGblast setup. all the executables are in the path, and I have already placed the database for humans in the...
Quite a lot has changed in Networkx v2.0 (https://networkx.github.io/documentation/stable/release/migration_guide_from_1.x_to_2.0.html) and it breaks `summarise`. For now, the requirements file specifies v1.11 exactly but we need to add v2.0 compatibility.
