... from 2017, not sure it's still applicable (https://github.com/vidjil/vidjil/issues/6)
Thanks for your time and help. I have spent some time to try to follow your advice but I still have some questions.
I have tried to use tools/fuse.py with the command, python tools/fuse.py --output mrd.vidjil --top 100 out/BCR01-01.fq.vidjil out/BCR23-01.fq.vidjil it gives me an error code : File "", line 1 python tools/fuse.py --output mrd.vidjil --top 100 out/BCR01-01.fq.vidjil out/BCR23-01.fq.vidjil ^ SyntaxError: invalid syntax BUT besides the error code, the more important concern to me is, fuse.py is a merge process of 2 vidjil files with top 100 clones, maybe we can make it to top 10,000 or even more(what if the target clone we are tracking is at very low concentration, maybe, let's say, number 10,000). After I got the mrd.vidjil file and I feed it to the web client, I still can only see the first 200, right? If the target clone is at number 30,000 in the after-treatment sample, I still can not see it in the web app. I didn't get the merged vidjil file due the above error, so I was just thinking in this way.
- For a full repertoire analysis, you have introduced me an -A option and this will process all the clones. I guess I could use the command like,
./vidjil -A -r 1 -g germline/homo-sapiens.g:IGH,IGH+,IGK data1/BCR01-01.fq.gz
I still could not use this vidjil output with the web client, right? Because it only can analysis top 200. So I have to use vdjtools by converting the vidjil file into vdjtools format and analysis from there. Because VDJtools will only use top clonotypes which have V/D/J detalization in the output, some clones lacking of V/D/J detalization will be dropped. So if our target clone is in this range, we can not see it, right?
- VDJtools supports parsing output Json files, what's Json file produced by vidjil, I only have .fa, .vidjil and a .windows.fa files. I have tried
Convert \ -S Vidjil BCR01-01.fq.vidjil output
the error messeges are,
Executing com.antigenomics.vdjtools.misc.Convert -S Vidjil BCR01-01.fq.vidjil output [Wed May 10 00:33:25 CDT 2017 Convert] Reading sample(s) [Wed May 10 00:33:25 CDT 2017 Convert] 1 sample(s) loaded [Wed May 10 00:33:25 CDT 2017 SampleStreamConnection] Loading sample BCR01-01.fq [ERROR] java.lang.NullPointerException, see _vdjtools_error.log for details
Thank you so much!