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Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data

In this study, we performed systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We generated SMART-seq2 data for 70 CD45- single cells, which were derived from two colorectal cancer patients (P0411 and P0413). The average sequencing depths of these cells were 1.4 million reads per cell. We also generated tumor and adjacent normal bulk WES data, as well as tumor bulk RNA-seq data for these patients.

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Data access policy of sequencing data from BIOPIC, Peking University.The DATA ACCESS AGREEMENT is provided at https://github.com/zhangyybio/single-T-cell-data-access. Applicants can request access to the data by directly downloading it or by sending an email to cancerpku@pku.edu.cn. The process that is used to approve an application includes verifying the institution, participants and research purposes of the application, and the authorization by EGA. In general this process will take about two weeks. In principal, any academic research institutions complying with the laws and bioethic regulation policies of China will be approved.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001003883 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00002797312 fq.gz 81.2 MB
EGAF00002797313 fq.gz 97.0 MB
EGAF00002797314 fq.gz 74.1 MB
EGAF00002797315 fq.gz 85.7 MB
EGAF00002797316 fq.gz 58.4 MB
EGAF00002797317 fq.gz 68.5 MB
EGAF00002797318 fq.gz 73.7 MB
EGAF00002797319 fq.gz 86.4 MB
EGAF00002797320 fq.gz 72.8 MB
EGAF00002797321 fq.gz 86.1 MB
EGAF00002797322 fq.gz 62.6 MB
EGAF00002797323 fq.gz 77.0 MB
EGAF00002797324 fq.gz 77.5 MB
EGAF00002797325 fq.gz 91.4 MB
EGAF00002797326 fq.gz 76.3 MB
EGAF00002797327 fq.gz 89.9 MB
EGAF00002797328 fq.gz 77.9 MB
EGAF00002797329 fq.gz 91.8 MB
EGAF00002797330 fq.gz 64.9 MB
EGAF00002797331 fq.gz 77.3 MB
EGAF00002797332 fq.gz 87.2 MB
EGAF00002797333 fq.gz 103.0 MB
EGAF00002797334 fq.gz 61.9 MB
EGAF00002797335 fq.gz 73.1 MB
EGAF00002797336 fq.gz 78.0 MB
EGAF00002797337 fq.gz 93.6 MB
EGAF00002797338 fq.gz 85.0 MB
EGAF00002797339 fq.gz 102.0 MB
EGAF00002797340 fq.gz 85.6 MB
EGAF00002797341 fq.gz 97.6 MB
EGAF00002797342 fq.gz 86.4 MB
EGAF00002797343 fq.gz 100.1 MB
EGAF00002797344 fq.gz 73.3 MB
EGAF00002797345 fq.gz 88.5 MB
EGAF00002797346 fq.gz 71.4 MB
EGAF00002797347 fq.gz 86.4 MB
EGAF00002797348 fq.gz 70.6 MB
EGAF00002797349 fq.gz 86.0 MB
EGAF00002797350 fq.gz 74.3 MB
EGAF00002797351 fq.gz 89.7 MB
EGAF00002797352 fq.gz 82.9 MB
EGAF00002797353 fq.gz 100.4 MB
EGAF00002797354 fq.gz 69.3 MB
EGAF00002797355 fq.gz 82.2 MB
EGAF00002797356 fq.gz 88.3 MB
EGAF00002797357 fq.gz 108.0 MB
EGAF00002797358 fq.gz 61.5 MB
EGAF00002797359 fq.gz 72.2 MB
EGAF00002797360 fq.gz 61.8 MB
EGAF00002797361 fq.gz 70.9 MB
EGAF00002797362 fq.gz 60.5 MB
EGAF00002797363 fq.gz 70.8 MB
EGAF00002797364 fq.gz 69.7 MB
EGAF00002797365 fq.gz 82.3 MB
EGAF00002797366 fq.gz 69.2 MB
EGAF00002797367 fq.gz 82.7 MB
EGAF00002797368 fq.gz 88.9 MB
EGAF00002797369 fq.gz 108.5 MB
EGAF00002797370 fq.gz 73.5 MB
EGAF00002797371 fq.gz 85.3 MB
EGAF00002797372 fq.gz 65.5 MB
EGAF00002797373 fq.gz 78.2 MB
EGAF00002797374 fq.gz 83.8 MB
EGAF00002797375 fq.gz 89.2 MB
EGAF00002797376 fq.gz 62.8 MB
EGAF00002797377 fq.gz 74.0 MB
EGAF00002797378 fq.gz 77.8 MB
EGAF00002797379 fq.gz 92.9 MB
EGAF00002797380 fq.gz 79.0 MB
EGAF00002797381 fq.gz 96.0 MB
EGAF00002797382 fq.gz 91.3 MB
EGAF00002797383 fq.gz 108.3 MB
EGAF00002797384 fq.gz 77.4 MB
EGAF00002797385 fq.gz 95.0 MB
EGAF00002797386 fq.gz 82.0 MB
EGAF00002797387 fq.gz 100.7 MB
EGAF00002797388 fq.gz 98.3 MB
EGAF00002797389 fq.gz 120.1 MB
EGAF00002797390 fq.gz 127.1 MB
EGAF00002797391 fq.gz 150.9 MB
EGAF00002797392 fq.gz 91.6 MB
EGAF00002797393 fq.gz 112.3 MB
EGAF00002797394 fq.gz 86.6 MB
EGAF00002797395 fq.gz 105.9 MB
EGAF00002797396 fq.gz 64.1 MB
EGAF00002797397 fq.gz 74.9 MB
EGAF00002797398 fq.gz 76.6 MB
EGAF00002797399 fq.gz 91.9 MB
EGAF00002797400 fq.gz 53.6 MB
EGAF00002797401 fq.gz 64.2 MB
EGAF00002797402 fq.gz 45.9 MB
EGAF00002797403 fq.gz 54.6 MB
EGAF00002797404 fq.gz 64.8 MB
EGAF00002797405 fq.gz 78.8 MB
EGAF00002797406 fq.gz 60.1 MB
EGAF00002797407 fq.gz 73.5 MB
EGAF00002797408 fq.gz 54.2 MB
EGAF00002797409 fq.gz 64.9 MB
EGAF00002797410 fq.gz 59.0 MB
EGAF00002797411 fq.gz 70.4 MB
EGAF00002797412 fq.gz 62.5 MB
EGAF00002797413 fq.gz 74.8 MB
EGAF00002797414 fq.gz 81.7 MB
EGAF00002797415 fq.gz 100.7 MB
EGAF00002797416 fq.gz 87.7 MB
EGAF00002797417 fq.gz 108.1 MB
EGAF00002797418 fq.gz 96.5 MB
EGAF00002797419 fq.gz 117.0 MB
EGAF00002797420 fq.gz 83.7 MB
EGAF00002797421 fq.gz 102.4 MB
EGAF00002797422 fq.gz 98.0 MB
EGAF00002797423 fq.gz 120.2 MB
EGAF00002797424 fq.gz 73.2 MB
EGAF00002797425 fq.gz 90.8 MB
EGAF00002797426 fq.gz 85.2 MB
EGAF00002797427 fq.gz 101.8 MB
EGAF00002797428 fq.gz 81.8 MB
EGAF00002797429 fq.gz 99.3 MB
EGAF00002797430 fq.gz 83.6 MB
EGAF00002797431 fq.gz 101.8 MB
EGAF00002797432 fq.gz 85.2 MB
EGAF00002797433 fq.gz 103.1 MB
EGAF00002797434 fq.gz 79.5 MB
EGAF00002797435 fq.gz 95.1 MB
EGAF00002797436 fq.gz 77.4 MB
EGAF00002797437 fq.gz 93.3 MB
EGAF00002797438 fq.gz 87.1 MB
EGAF00002797439 fq.gz 105.3 MB
EGAF00002797440 fq.gz 87.9 MB
EGAF00002797441 fq.gz 109.2 MB
EGAF00002797442 fq.gz 85.7 MB
EGAF00002797443 fq.gz 106.3 MB
EGAF00002797444 fq.gz 84.6 MB
EGAF00002797445 fq.gz 104.5 MB
EGAF00002797446 fq.gz 96.5 MB
EGAF00002797447 fq.gz 112.6 MB
EGAF00002797448 fq.gz 92.8 MB
EGAF00002797449 fq.gz 115.0 MB
EGAF00002797450 fq.gz 83.7 MB
EGAF00002797451 fq.gz 102.1 MB
EGAF00002797452 fq.gz 6.4 GB
EGAF00002797453 fq.gz 7.6 GB
EGAF00002797454 fq.gz 2.9 GB
EGAF00002797455 fq.gz 3.2 GB
EGAF00002797456 fq.gz 6.5 GB
EGAF00002797457 fq.gz 7.7 GB
EGAF00002797458 fq.gz 2.9 GB
EGAF00002797459 fq.gz 3.4 GB
EGAF00002797460 fq.gz 2.9 GB
EGAF00002797461 fq.gz 3.4 GB
150 Files (58.8 GB)