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توضیحات

Processing Drop-seq, 10X(3prime) and inDrop RNA-seq dataset

ویژگی	مقدار
سیستم عامل	-
نام فایل	baseqDrops-2.0
نام	baseqDrops
نسخه کتابخانه	2.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Xiannian Zhang
ایمیل نویسنده	friedpine@gmail.com
آدرس صفحه اصلی	https://gene.pku.edu.cn
آدرس اینترنتی	https://pypi.org/project/baseqDrops/
مجوز	-

# baseqDrops A versatile pipeline for processing dataset from 10X, indrop and Drop-seq. ## Install baseqDrops We need python3 and a package called: baseqDrops, which could be installed by: pip install baseqDrops After install, you will have a runnable command `baseqDrops` It is recommend for the computer or server to have memory >= 30Gb and CPU cores >=8 for efficient processing; ## Configuration file The following software or resources are required: + `star`: STAR software, for fast alignment of RNA-Seq data to the genome; + `samtools`: For sorting the aligned bam file (version >=1.6); + `whitelistDir`: The barcode whitelist files for indrop and 10X should be placed under whitelistDir. These files could bed downloaded from https://github.com/beiseq/baseqDrops/tree/master/whitelist; + `cellranger_ref_<genome>`: The key process of read alignment and tagging to genes are inspired and borrowed from the open source cellranger pipeline(https://github.com/10XGenomics/cellranger). The references of genome index and transcriptome can be downloaded from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. In the config file, the directory of cellranger references is named as `cellranger_<genome>`. While running command, the configures are recorded in the file called `config_drops.ini`: [Drops] samtools = /path/to/samtools star = /path/to/STAR whitelistDir = /path/to/whitelist_file_directory cellranger_ref_hg38 = /path/to/reference/refdata-cellranger-GRCh38-1.2.0/ ## For Help Informations baseqDrops run-pipe --help ## Process Steps 1. `Cell Barcode Counting`: Counting the existed barcodes in dataset. This will generate a file named: barcode_count_<sample>.csv; 2. `Cell Barcode Correction, Aggregating and Filtering`: Correcting the cell barcodes within 1bp mismatch and then aggregating, filtering the barcode by minimum number of reads (default 5000), this will generate a valid barcode list named: barcode_stats_<sample>.csv; 3. `Split the Reads of Valid Cell Barcodes`: The raw pair-end raw reads are splitted to 16 single-end files for multiprocessing according to the 2bp prefix of the barcode; The folder of barcode_splits contains files like: split.<sample>.<AA|AT|AC|AG...|GG>.fq; 4. `Alignment to Genome using STAR`: Several (defined by --parallel/-p) STAR programs run at the same time, the results will be at folder named as star_align; The bam files are further sorted by sequence header; 5. `Reads Tagging`: Tagging the reads alignment position to the corresponding gene name; 6. `Generating Expression Table`: Both the expression table quantified by UMI (Result.UMIs.<sample>.txt) and raw read count (Result.Reads.<sample>.txt) will be generated; ## Run Pipeline These parameters should be provided: (or run: baseqDrops run-pipe --help for information) + `--outdir/-d`: Output path (default ./, the result will be stored in ./<name>); + `--config`: Path to the config file; + `--genome/-g`: Genome version [hg38/mm38/hgmm]; + `--protocol/-p`: [10X|indrop|dropseq]; + `--minreads`: Minimum reads required for a barcode; + `--name/-n` : Name of sample, a folder of <outdir>/<name> will be created and be the main directory; + `--parallel` : The number of STAR and tagging processes runs at the same time (default is 4, need more memory for larger parallel number); + `--fq1/-1`: Path of Pair-end 1 sequencing file; + `--fq2/-2`: Path of Pair-end 2 sequencing file; + `--top_million_reads`: For huge dataset, you can choose to use part of the data for a quick look, the reads exceeding N million of reads will be skipped; If your data is human origin and `cellranger_ref_hg38` has been defined in configuration file, you can run: baseqDrops run-pipe --config ./config_drops.ini -g hg38 -p 10X --minreads 1000 -n 10X_test -1 10x_1.1.fq.gz -2 10x.2.fq.gz -d ./ ## Run by Single Steps We also provide step-wise ways for running the pipeline, all the parameters should be provided as described above, an extra "--step" should be provided, for example: baseqDrops run-pipe --config ./config.ini -g hg38 -p dropseq --minreads 1000 -n dropseq2 --top_million_reads 20 -1 dropseq_1.1.fq.gz -2 dropseq.2.fq.gz --step count -d ./ The steps are listed: + `Cell Barcode Counting`: --step count + `Cell Barcode Correction, Aggregating and Filtering`: --step stats + `Split the Reads of Valid Cell Barcodes`: --step split + `Alignment to Genome using STAR`: --step star + `Reads Tagging` : --step tagging + `Generating Expression Table`: --step table ## Contact For any questions, please email to: friedpine@gmail.com

نیازمندی

مقدار	نام
-	click
-	configparser
-	matplotlib
-	numpy
-	pandas
-	pysam
xtr	check-manifest;
xtr	coverage;

نحوه نصب

نصب پکیج whl baseqDrops-2.0:

pip install baseqDrops-2.0.whl

نصب پکیج tar.gz baseqDrops-2.0:

pip install baseqDrops-2.0.tar.gz