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The pipleline of single cell RNA

The pipleline of single cell RNA

作者: 花生米yangyang | 来源:发表于2022-08-03 12:52 被阅读0次

    1 Alignment (fastq->bam)

    (1) 10X Genomics fastq data

    If we get fastq data from 10X Genomics, we can do alignment using cellranger with the parameter:

    cellranger count \
    --id=run_count_1kpbmcs \
    --fastqs=/home/01.example_script/02.cellranger/pbmc_1k_v3_fastqs\
    --sample=pbmc_1k_v3\
    --transcriptome=/home/01.example_script/02.cellranger/refdata-gex-GRCh38-2020-A/
    

    id means the output folder name .
    fastqs means the folder which contains the input fastq files.
    sample means sample id
    transcriptome means reference file download from cellranger website.
    Then we can get a output folder named run_count_1kpbmc. The files in the run_count_1kpbmc are as below:

    图片.png
    The files in the out folder are as below:
    图片.png
    we used the possorted_genome_bam.bamand filtered_feature_bc_matrix as input files for further analysis.
    (2) non 10X Genomics fastq data
    we can do aligment use the software hisat2 with parameter :
    /hisat2 \
    -q \
    -x /02.Hisat2/01.prepare_data/grcm38/genome\
    -U /03.downloaddata2-2022.7.27/01.fastq_dta/SRR3557021.fastq \
    -S /03.downloaddata2-2022.7.27/02.hisat2_align_bam/SRR3557021/SRR3557021.sam\
    samtools view \
    -bS /03.downloaddata2-2022.7.27/02.hisat2_align_bam/SRR3557021/SRR3557021.sam > /nfs/public/liuyang/03.downloaddata2-2022.7.27/02.hisat2_align_bam/SRR3557021/SRR3557021.bam
    /usr/bin/samtools sort /nfs/public/liuyang/03.downloaddata2-2022.7.27/02.hisat2_align_bam/SRR3557021/SRR3557021.bam -o /nfs/public/liuyang/03.downloaddata2-2022.7.27/02.hisat2_align_bam/SRR3557021/SRR3557021.sort.bam
    rm -r /nfs/public/liuyang/03.downloaddata2-2022.7.27/02.hisat2_align_bam/SRR3557021/SRR3557021.sam
    

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