uubram

Dear Vadim, Thank you for your interest in RTCR! As per your request, see below for an example output file. I'm not sure if it's helpful, but RTCR includes a...

Dear Vadim, As of today, the output of RTCR conforms to the Adaptive Immune Receptor Repertoire (AIRR) Community format. Since immunarch supports the AIRR format, it is already able to...

According to the error in the log, the child process was killed via SIGKILL. This is probably a result of the system running out of memory and the Out Of...

I do not think that there is something wrong with your input data, but that you're still running out of memory. The error that 'rqi.dat' was not found, is probably...

Hi Ying, 1. If you mean in how many input sequences a TCR was identified, then you can use the following command: `rtcr Convert -i r.dat | awk -F"\t" 'NR>1{c+=$15}END{print...

Thank you for your kind words. See my reply to your [ticket](https://github.com/immunomind/immunarch/issues/91) for an example dataset. Best, Bram

You're welcome! I will close this issue once I have the okay from your end.

Hi Magdalena, In principle there should be no differences in results when RTCR is run twice on the same fastq file. However, results may be affected by the order in...

I think your scenario is effectively a 'low read count' situation (i.e. low read count for TCRs). It should be possible to use RTCR without any changes to its settings....

It is possible to load your own reference genes using the `--ref` option of the `rtcr run` command. Supposing your genes are in [IMGT reference fasta format](https://www.imgt.org/vquest/refseqh.html), included [here](https://github.com/uubram/RTCR/files/12567941/convert_IMGT.zip) is...