timothy-barry / sceptre-pipeline-1 Goto Github PK

Hello,

First, thank you for the great tool for multiplexing CRISPRi screen. I would want to use sceptre for my dataset of multiplex gRNA (10-15gRNA/cells) for a pool of 1000 gRNA. I was able to follow your tutorial for small dataset, but am stuck now for the large scale.
Can you please provide more instructions how to generate the required input files using ondisc?
Thank you,
Linh

1. Allow user to include offsets in formula string.
2. Add an option to use a Gaussian to fit the resampling distribution?

Hi Timothy,
I am completely new in bioinformatics and now I have data on 10X CRISPR screen to analyse. I will like to use sceptre Nextflow tool. Before using my data I will like to go through the "Gasperini data 2019". I am not sure where to get the data from or how did you format the data submitted on GEO: GSE120861 from the paper.
Thanks

Hi Tim,

I am having some trouble with the Nextflow pipeline, I am getting diffent genes and gRNA groups failing precomputations every time (a different one) with the same error "ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory." .

Any help with this will be appreciated.

N E X T F L O W ~ version 22.10.6
Launching /home/ubuntu/sceptre-pipeline/main.nf [suspicious_poisson] DSL2 - revision: b0cd4d6075
executor > local (98)
executor > local (98)
[2b/48fb6c] process > check_inputs [100%] 1 of 1 ✔
[dd/65e4fa] process > perform_gene_precomputation (60) [ 3%] 6 of 189, failed: 6
[93/1d9dc0] process > perform_grna_precomputation (4) [ 0%] 0 of 45
[- ] process > join_gene_precomputations -
[- ] process > join_grna_precomputations -
[- ] process > perform_pairwise_association_test -
[- ] process > combine_results -
Error executing process > 'perform_gene_precomputation (47)'

Caused by:
Process perform_gene_precomputation (47) terminated with an error exit status (1)

Command executed:

perform_precomputation.R "gene" multimodal_metadata_fp gene_odm_fp gene_to_pod_id_map 47 3 crt

Command exit status:
1

Command output:
[1] "Regressing gene ENSG00000111237 onto covariates."

Command error:
[1] "Regressing gene ENSG00000111237 onto covariates."
Error in extract_matrix(.) :
ondisc_matrix has 0 rows or columns; cannot extract sub-matrix into memory.
Calls: ... .local -> [[ -> [[ -> .local -> %>% -> extract_matrix
Execution halted

Work dir:
/data/sceptre_nextflow_top2/work/ad/2d146cb518c1f17239fd08d826c78f

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line