Frequently asked questions

Possibility to consider multiple control

User can redefine the genotype; in the step8, add /job_info/parameters/step8_par.txt, add new_genotype='YES and redefine the labels:

new_genotype='YES'
old_antibody_label=c('B0251-TotalSeqB','B0252-TotalSeqB','B0253-TotalSeqB','B0254-TotalSeqB','B0255-TotalSeqB','B0256-TotalSeqB')
new_antibody_label=c('AIW002','SNCA-A53T','GBA-KO','Parkin-KO','PINK1-KO','SNCA-KO')

How to skip the integration step

If you have a sole sample, there is no need for the integration step; once you run step 4, go to step 6 and add par_skip_step5='YES' to the step 6 parameter, /job_info/parameters/step6_par.txt.

Can we run without cellraanger.

if you have the matrix file, .......

error: Batch job submission failed: Requested node configuration is not available

If you get the above error, navigate to the scrnabox_config.ini file in ~/working_directory/job_info/configs and adjust the Job parameters for the Analytical Step that produced the error. Make sure to uncomment the corresponding lines in the configuration file. For example, if you get the error in Step 2, navigate to the configuration file and you will see the following.

############# [step2]
# THREADS_ARRAY["step_2"]=10
# MEM_ARRAY["step_2"]=16g
# WALLTIME_ARRAY["step_2"]=00-05:00

To resolve the error, uncomment the lines and change the values. For instance:

############# [step2]
THREADS_ARRAY["step_2"]=4
MEM_ARRAY["step_2"]=10g
WALLTIME_ARRAY["step_2"]=00-05:00

Step 3: Error in { : task 1 failed - "No cells found"

adjust the filtering parameters, this means that none of the cells in the users experiment pass all of the filtering thresholds.

how to edit text files in the terminal

I have Seurat object but I want to start at Step 2?