About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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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.

Request Access

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. To get the access to raw data, an agreement must be made first. Please fill in the form in https://github.com/zhangyybio/single-T-cell-data-access, and send me (cancerpku@pku.edu.cn) the document with signatures added. Particularly,in the page 4 of the agreement, table "Agreed for User Institution" should contain the signature of the person who can represent your institution, such as institution director

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