problems about celescope

[Chenjunjie1996]

Could you please show me shell script and results in 02.convert directory?

[33Dr]

Hi CHenjunjie1996,,
thanks for your kind reply.

multi_convert10X
--mapfile ./rna.mapfile
--chemistry flv_rna
--thread 8
--mod shell
--soft_path home/path/CeleScope/cellranger

celescope convert10X sample --outdir .//test1/00.sample --sample test1 --thread 8 --chemistry flv_rna --fq1 /home/path/CeleScope/mymapfiles/rna_1.fastq.gz
celescope convert10X barcode --outdir .//test1/01.barcode --sample test1 --thread 8 --chemistry flv_rna --lowNum 2 --fq1 /home/path/CeleScope/mymapfiles/rna_1.fastq.gz --fq2 /home/path/CeleScope/mymapfiles/rna_2.fastq.gz
celescope convert10X convert --outdir .//test1/02.convert --sample test1 --thread 8 --soft_path home/path/CeleScope/cellranger --tenX_chemistry V2 --fq2 .//test1/01.barcode/test1_2.fq
celescope convert10X cellranger --outdir .//test1/03.cellranger --sample test1 --thread 8 --soft_path home/path/CeleScope/cellranger --mem 10 --fqs_dir .//test1/02.convert

Convert directory folder is empty

Best!

[Chenjunjie1996]

You can try following script:
multi_convert10X --chemistry flv_rna --mapfile ./rna.mapfile --thread 8 --soft_path "/soft/cellranger/cellranger-6.1.2/cellranger" --ref_path "/soft/cellranger/refdata-gex-GRCh38-2020-A"

• Specifying the soft_path and ref_path manually. soft_path and ref_path require absolute path of cellranger program and
  and reference data files. Download pages: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
• Chemistry can be detected automatically in latest celescope version. If you have installed latest celescope version, you can ignore "--chemistry" parameter

[33Dr]

Thanks Chenjunjie1996,

I will try following your advices.
Best

[33Dr]

What exactly is --soft_path: soft path for cellranger and --ref_path reference path for cellranger?

[Chenjunjie1996]

You can refer to step1 ans step 2 of https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
Soft path and reference path are absolute path of cellranger and reference data files after unpacking.
For example:

• 
  --soft_path "/SGRNJ03/randd/cjj/soft/cellranger/cellranger-6.1.2/cellranger"

• 
  --ref_path "/SGRNJ03/randd/cjj/soft/cellranger/refdata-gex-GRCh38-2020-A"

[33Dr]

Thank you very much, Chenjunjie1996, it worked now.
Best

[33Dr]

Dear all,

to run multi convert 10X itself worked very well.

But I have another problem now. I tried to convert the fastq files which derive from GEXSCOPE to the 10X format running multi convert 10x. When I compare the scopeV2.2.1 output with the Cellranger output after running multi convert 10X, I can observe huge differences in Mean Reads per Cell, Total Genes and Median Genes per Cell.

Could you please help me?
Thanks in advance,

Best

[Chenjunjie1996]

Could you please send the celescope and cellranger HTML reports to me?
[email protected]

[33Dr]

Thanks for your help, Chenjunjie. I sent it to you.
Best

[33Dr]

I used the following script:

multi_convert10X --chemistry flv_rna --mapfile ./rna.mapfile --thread 8 --mod shell --soft_path "/home/opt/cellranger-7.1.0/cellranger" --ref_path "/home/opt/cellranger-7.1.0/refdata-gex-GRCh38-2020-A"

[Chenjunjie1996]

multi_convert10X --mapfile ./rna.mapfile --thread 8 --mod shell --soft_path "/home/opt/cellranger-7.1.0/cellranger" --ref_path "/home/opt/cellranger-7.1.0/refdata-gex-GRCh38-2020-A"

[33Dr]

Thank you so much for your help and support. It worked!