cellranger vdj

cellranger VDJ 第一次处理数据

#常用参数：

Argument	Description
--id	A unique run ID string: e.g. sample345
--fastqs	Path of the FASTQ folder generated by cellranger mkfastq e.g. /home/jdoe/runs/HAWT7ADXX/outs/fastq_path Can take multiple comma-separated paths, which is helpful if the same library was sequenced on multiple flowcells. Doing this will treat all reads from the library, across flowcells, as one sample.
--reference	Path to the Cell Ranger V(D)J compatible reference e.g. /opt/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0. If --denovo is specified, this argument is optional.
--sample	Sample name as specified in the sample sheet supplied to mkfastq. Can take multiple comma-separated values, which is helpful if the sample was sequenced on multiple flowcells and the sample name used (and therefore fastq file prefix) is not identical between them. Doing this will treat all reads from the library, across flowcells, as one sample.

#常用可选参数：

Argument	Description
--denovo	Do not use the V(D)J reference during the assembly process. If specified, --reference is optional, however if --denovo is specified but --reference is not, then --inner_enrichment_primers must be specified. The --denovo option is most useful for full de novo assembly without a V(D)J reference. If you have a V(D)J reference, using --denovo will typically yield similar but slightly degraded results.
--inner-enrichment-primers	Name of a file containing primer sequences, one per line, that were used to enrich cDNA for V(D)J sequences. If there are two sets of primers, that should be the innermost reverse PCR primers, that are complementary to a constant region. For example for human TCR, the file having two lines:AGTCTCTCAGCTGGTACACGTCTGATGGCTCAAACACAGC would be equivalent to the default primers (if this option were not specified). However normally this option is used only for species other than human or mouse for which primers are not provided by 10x Genomics. All the provided primers may be found here.

–localcores:

–localmem:

–lanes:

Argument	Description
--chain	Force the analysis to be carried out for a particular chain type. The accepted values are:auto for autodetection based on TR vs IG representation (default),TR for T cell receptors,IG for B cell receptors,Use this in rare cases when automatic chain detection fails.

##运行

time nohup cellranger vdj --id=test_of_vdj \ #name of output directory 
--fastqs=/public/home/djs/cell_ranger_test/sc5p_v2_hs_B_1k_multi_5gex_b_fastqs/sc5p_v2_hs_B_1k_b_fastqs \ #path of input
--reference=/public/home/djs/cell_ranger_test/vdj_reference \ #vdj reference
--sample=sc5p_v2_hs_B_1k_b \ #option of sample or combine some sample
#--lanes=
--localcores=32 \ #limit of core of cpu
--localmem=100 & \ #limit of memory of GB