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vals
Tools for processing UMI RNA-tag data
Running the `test.sh` file on the v1.0.8 version leads to `KeyError` in test11 and test14. Pertinent log output: ```bash INFO:umis.umis:Transforming examples/STRT-Seq/dualindex_example_1.fastq. INFO:umis.umis:Detected dual cellular indexes. INFO:umis.umis:Detected dual UMI. Traceback (most...
Hi @vals, Do you think you could turn on Travis for this repo, or make me a co-owner so I can do it? It would be nice to run the...
Hi, I am currently testing umis for our 10XGenomics data. fasttagcount crashes when no cb_histogram is provided: File "build/bdist.linux-x86_64/egg/umis/umis.py", line 829, in fasttagcount AttributeError: 'NoneType' object has no attribute 'index'...
Hi, I used `umis cb_histogram` to calculate reads count for each cell and then chose a count cutoff based on that. For the downstream analysis, such as pseudo-align and count...
I was speaking to Nuno at the Expression Atlas who said our format for Fastq headers is not compatible with CASAVA standard. I think it would make sense to change...
I was wondering if you had considered merging UMIs that might be erroneous copies, eg as outlined in this [blog](https://cgatoxford.wordpress.com/2015/08/14/unique-molecular-identifiers-the-problem-the-solution-and-the-proof/) post. > The use of UMIs [...] would work perfectly...
Hi, in our Debian development Git you can find a [patch for a Python3.12 syntax issue](https://salsa.debian.org/med-team/umis/-/blob/master/debian/patches/pyhon3.12-syntax.patch?ref_type=heads) and a [patch for Pandas 2.0](https://salsa.debian.org/med-team/umis/-/blob/master/debian/patches/read_csv-no_squeeze.patch?ref_type=heads). Feel free to take over these patches in...
