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Home / scRNAseq_test
Name Modified Size InfoDownloads / Week
Parent folder
README.txt 2022-10-15 1.0 kB
0
possorted_genome_bam.bam 2022-10-15 32.9 MB
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test_sample_S1_L001_R1_001.fastq.gz 2022-10-15 2.9 kB
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test_sample_S1_L001_R2_001.fastq.gz 2022-10-15 7.2 kB
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test_sample_S1_L001_I1_001.fastq.gz 2022-10-15 1.5 kB
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possorted_genome_bam.bam.bai 2022-10-15 30.9 kB
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Totals: 6 Items   33.0 MB 0 
These files were used to test the following 4 RSeQC programs:

1. sc_bamStat.py
2. sc_editMatrix.py
3. sc_seqLogo.py
4. sc_seqQual.py


fastq files
============

The three fastq files:
* test_sample_S1_L001_I1_001.fastq.gz
* test_sample_S1_L001_R1_001.fastq.gz
* test_sample_S1_L001_R2_001.fastq.gz

were created following this procedure (see also: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_fq):

1. Download and install Illumina’s *bcl2fastq2* command if it is not available. 
2. wget https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz
3. wget https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv
4. tar -zxvf cellranger-tiny-bcl-1.2.0.tar.gz
5. cellranger mkfastq --id=tutorial_walk_through --run=cellranger-tiny-bcl-1.2.0 --csv=cellranger-tiny-bcl-simple-1.2.0.csv 

the three fastq files were located under: H35KCBCXY


BAM file
============
The BAM file was created by cellranger test run

* cellranger testrun --id=tiny
Source: README.txt, updated 2022-10-15