A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi Guys,

I’m running crisperseq for the first time and getting stuck running my own dataset and I was wondering if you might be able to give me a few pointers ?

(1) In the library file, is the first column as a target transcript sequence needed (it seems that this is the same as the sgRNA sequence +/- a few base pairs ?  or can I replace this with an ID as mentioned in the manual ?



(2) I somehow get this error message and wonder if you might now what this error means

`NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE (ALL-54_Dexamethasone_vs_ALL-54_Saline)` terminated with an error exit status (1)


(3)   Could the error come from the design matrix which is automatically generated ?
Samples    baseline             ALL.54_Dexamethasone_vs_ALL.54_Saline    ALL-54_Dexamethasone_vs_ALL-54_Saline
ALL-54_Saline        1            0            NA
ALL-54_Dexamethasone   1            0            1


Thank you very much !

Cheers,
Dominik

Hi Dominik!

Could you give me your contrast file? I think the matrix file that is generated is indeed faulty

I’m not sure about question 1)
I think it is needed as it is used for mapping, but you can always try it out with your ID and see if you get a mapped count table