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WubingZhang / MAGeCKFlute

Integrative analysis pipeline for pooled CRISPR functional genetic screens
https://github.com/WubingZhang/MAGeCKFlute
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MLE subcommand usage question #1

Closed YichaoOU closed 4 years ago

YichaoOU commented 5 years ago

Following the nature protocols paper, I have two conditions: A & B, and the Day 0 info. I want to compare A & B. I made the design matrix like Table 5.

When I got the mle results, it basically gave me two beta values; namely A vs. Day 0 and B vs. Day 0, right?

What if I just want a beta value for A vs. B? Is it appropriate to treat B as Day 0 and then the design matrix will just have A and B?

Thanks, Yichao

jinyanyouyu1994 commented 4 years ago

How to deal with the paired-end fastq file? my code is :mageck count -l library_mageck.csv -n s2 --sample-label NC85_T1,NC85_T2,NC85_96_R1,NC85_96_R2 --fastq 85-T1_combined_R1.fastq.gz,85-T1_combined_R2.fastq.gz 85-T2_combined_R1.fastq.gz,85-T2_combined_R2.fastq.gz 85-96-R1_combined_R1.fastq.gz,85-96-R1_combined_R2.fastq.gz 85-96-R2_combined_R1.fastq.gz,85-96-R2_combined_R2.fastq.gz when I try to use the --fastq-2, there is an error: mageck count: error: one of the arguments --fastq -k/--count-table is required. I don't understand the count-table?

WubingZhang commented 4 years ago

Hi,

Following the nature protocols paper, I have two conditions: A & B, and the Day 0 info. I want to compare A & B. I made the design matrix like Table 5.

When I got the mle results, it basically gave me two beta values; namely A vs. Day 0 and B vs. Day 0, right?

What if I just want a beta value for A vs. B? Is it appropriate to treat B as Day 0 and then the design matrix will just have A and B?

Thanks, Yichao

Hi,

You can make a design matrix like below:

Day0 1 0 0 A 1 1 0 B 1 1 1

WubingZhang commented 4 years ago

How to deal with the paired-end fastq file? my code is :mageck count -l library_mageck.csv -n s2 --sample-label NC85_T1,NC85_T2,NC85_96_R1,NC85_96_R2 --fastq 85-T1_combined_R1.fastq.gz,85-T1_combined_R2.fastq.gz 85-T2_combined_R1.fastq.gz,85-T2_combined_R2.fastq.gz 85-96-R1_combined_R1.fastq.gz,85-96-R1_combined_R2.fastq.gz 85-96-R2_combined_R1.fastq.gz,85-96-R2_combined_R2.fastq.gz when I try to use the --fastq-2, there is an error: mageck count: error: one of the arguments --fastq -k/--count-table is required. I don't understand the count-table?

Hi,

Could you post this question in google group (https://groups.google.com/forum/#!forum/mageck) so that Wei can deal with it?

Thanks1