tracer
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Teichlab
TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
In my application I have need downstream of the "full" TCR sequence, including leader all the way to the constant region. Is it conceivable to alter the references (pad out...
Hi : When I run the tracer test, there was a futurewarning in the final step of ##Filtering by read count##. " Software/anaconda2/lib/python2.7/site-packages/scipy/stats/stats.py:1713: FutureWarning: Using a non-tuple sequence for multidimensional...
Hi, I'm going to testing TraCer by runing `tracer test`.But everytime it returns an error after printing runing IgBlast,fully copy as follows: `##Running IgBLAST## CMD failed: Traceback (most recent call...
Hi! Thanks a lot for this wonderful work! My colleague did some analysis using tracer and we're a little bit confused about the output file 'cell_data.csv' and 'recombinants.txt'. It seems...
Hello, I am helping @hkoohy to install tracer, and was wondering whether somebody has been working on a conda package for it. If not, I am happy to build a...
The `--loci` command line argument takes a space-separated list of locus names. This means that it *must* be followed by another command line option so that argparse knows when to...
As we discussed in Teichlab/bracer#21 , when using 10X Genomics outputs, reads should be split by cell and then called their VDJ types using `bracer assembly`'s `--assembled_file` option. I suppose...
`cell2` and `cell3` test outputs need to be regenerated using the new code that reports CDR3 sequences
Hi Mike _et al._! Just wondering if there are plans to update the Docker image to IgBLAST 1.8? We're seeing some differences in performance/reconstruction between our local version of the...
Hi, I'm having an issue running igblastn. Every time I do, I get an error saying an annotation database in internal_data could not be found. I did follow the installation...
