majiq build on many human samples?

[Welmoed van Zuiden]

Hello,

I have hundreds of bam files, each one derived from postmortem tissue from another human individual, and I wonder how to run the build step. I wish to compare two groups, but each group has a few hundred samples in them. So when I set up the [experiment] part of the config file, dividing all samples over two groups, I got the error pasted below (sqlite3.IntegrityError: UNIQUE constraint failed: experiment.name). When I tried setting min-experiments to 1 and leaving out the [experiment] part of the config file, there were 0 LSVs detected.

Could you help me set the parameters in the correct way? Each sample is a unique individual with a unique ID thus unique bam file name. It will be enough for an LSV to pass if it is detected in 1 sample. I would also love to get tips / reference to documentation for the quantification part with this large amount of data.

Best,

Welmoed

  File "/home/labs/hornsteinlab/welmoed/anaconda3/envs/majiq/bin/majiq", line 8, in <module>
    sys.exit(main())
  File "/home/labs/hornsteinlab/welmoed/anaconda3/envs/majiq/lib/python3.10/site-packages/rna_majiq/run_majiq.py", line 641, in main
    args.func(args)
  File "rna_majiq/src/build.pyx", line 649, in rna_majiq.src.build.build
  File "/home/labs/hornsteinlab/welmoed/anaconda3/envs/majiq/lib/python3.10/site-packages/rna_majiq/src/basic_pipeline.py", line 13, in pipeline_run
    return pipeline.run()
  File "rna_majiq/src/build.pyx", line 657, in rna_majiq.src.build.Builder.run
  File "rna_majiq/src/build.pyx", line 671, in rna_majiq.src.build.Builder.builder
  File "rna_majiq/src/build.pyx", line 566, in rna_majiq.src.build._core_build
  File "rna_majiq/src/build.pyx", line 418, in rna_majiq.src.build.init_splicegraph
  File "rna_majiq/src/build.pyx", line 419, in rna_majiq.src.build.init_splicegraph
  File "/home/labs/hornsteinlab/welmoed/anaconda3/envs/majiq/lib/python3.10/site-packages/rna_voila/api/splice_graph.py", line 104, in experiment_names
    self.conn.executemany('''
sqlite3.IntegrityError: UNIQUE constraint failed: experiment.name

[San Jewell]

Hello Welmoed,

Could you share the config.ini file with me? Basically it just sounds like there is a repeated group name under experiments ; it should be something like this:

[experiments]

group1=sample1, sample2, sample3, ...... (half of your hundreds of bam files)

group2=sample100, sample101, sample102, ...... (the other half)

I think possibly you had named "group1" and "group2" the same here?

Let me know if it makes sense.

Thanks,

-San