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tsailabSJ / changeseq

CHANGE-seq analysis pipeline
GNU Affero General Public License v3.0
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file missing #6

Closed lisiang closed 3 years ago

lisiang commented 4 years ago

I had some problems while researching CHANGE seq, When I run "changeseq.py all - manifest.YAML" an error appears The error code is: "usage: changeseq.py all [-h] --manifest MANIFEST [--sample SAMPLE] changeseq.py all: error: argument --manifest/-m is required" I don't understand what caused this error.

When I was running the "manifest.yaml" provided on GitHub https://github.com/tsailabSJ/changeseq
some necessary files are missing "read1: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/1_S1_L001_R1_001.fastq.gz read2: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/1_S1_L001_R2_001.fastq.gz controlread1: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/4_S4_L001_R1_001.fastq.gz controlread2: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/4_S4_L001_R2_001.fastq.gz

read1: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/2_S2_L001_R1_001.fastq.gz read2: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/2_S2_L001_R2_001.fastq.gz controlread1: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/4_S4_L001_R1_001.fastq.gz controlread2: /data/joung/sequencing_fastq/150902_M01326_0235_000000000-AHLT8/fastq/4_S4_L001_R2_001.fastq.gz"

If it is convenient, could you please upload the file you used to run the above "manifest.yaml"

YichaoOU commented 4 years ago

Hello,

Your command changeseq.py all - manifest.YAML is not valid, because just like the error message said, -m is required, you missed -m. So it should be changeseq.py all -m manifest.YAML.

In terms of testing, go to the test folder:

cd changeseq/test

changeseq.py all --manifest CIRCLEseq_MergedTest.yaml

Testing dataset is provided in that folder.

You can find some real change-seq data here: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA625995

I think the sgRNA info is provided in the supplementary files.

Let me know if you need more help.

Yichao