Alignment BAM files and gene count files of the Illumina Sequencing Data (10 tumor samples)
Reads were processed with the RNA-seq workflow 1.3.0 developed by the DKFZ Omics IT and Data Management Core Facility (https://github.com/DKFZ-ODCF/RNAseqWorkflow). First, FASTQ reads were aligned via two-pass alignment using STAR 2.5.3a. The STAR index was generated from the 1000 Genomes assembly and GENCODE Version 19 gene models with a sjdbOverhang of 200. Duplicate marking of the resultant main alignment file was done with sambamba 0.6.5. Gene-specific read counting was performed using featureCounts (from Subread 1.5.1) over exon features based on GENCODE Version 19 gene models. Both reads of a paired fragment were used for counting, and the quality threshold was set to 255, indicating that STAR found a unique alignment. Strand-specific counting was also used. For RPKM and TPM calculations, all genes on chromosomes X and Y, the mitochondrial genome, as well as rRNA and tRNA genes were omitted as they are likely to introduce library size estimation biases.
- 10 samples
- DAC: EGAC00001000452
Data Transfer Agreement for the German Cancer Research Center
To request access to the dataset please start a Data Access Request via the EGA DAC Portal. You will receive a HIPO DACO Info Form by email to collect information about the request, which has to be filled completely and signed by your PI. Your request will be evaluated by the responsible Data Access Committee (DAC) and our Data protection department (and innovation management if required). As soon as a positive decision is made, you will be provided with a data transfer agreement (DTA). After the DTA has been fully signed, access to the requested data is granted. To ensure that the process can be completed as quickly as possible, please note the following points: 1. The request in the EGA portal must be made by the responsible PI. 2. The information in the EGA portal must match the information on the HIPO DACO Info Form. In particular, the email address and the requested data sets must match. It is also important that all requested data sets are also listed on the HIPO DACO Info Form. For-profit companies are charged a fee per request.
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 |
|---|---|---|
| EGAS00001006317 | Cancer Genomics |
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 | |
|---|---|---|---|---|
| EGAF00006211218 | tsv | 11.0 MB | ||
| EGAF00006211219 | bam | 74.2 GB | ||
| EGAF00006211220 | tsv | 11.2 MB | ||
| EGAF00006211221 | bam | 64.6 GB | ||
| EGAF00006211222 | tsv | 10.2 MB | ||
| EGAF00006211223 | bam | 11.2 GB | ||
| EGAF00006211224 | tsv | 10.4 MB | ||
| EGAF00006211225 | bam | 11.4 GB | ||
| EGAF00006211226 | tsv | 11.1 MB | ||
| EGAF00006211227 | bam | 57.1 GB | ||
| EGAF00006211228 | tsv | 9.9 MB | ||
| EGAF00006211229 | bam | 6.3 GB | ||
| EGAF00006211230 | tsv | 9.2 MB | ||
| EGAF00006211231 | bam | 8.9 GB | ||
| EGAF00006211232 | tsv | 10.1 MB | ||
| EGAF00006211233 | bam | 13.8 GB | ||
| EGAF00006211234 | tsv | 10.2 MB | ||
| EGAF00006211235 | bam | 8.3 GB | ||
| EGAF00006211236 | tsv | 10.1 MB | ||
| EGAF00006211237 | bam | 7.9 GB | ||
| EGAF00006211238 | bai | 6.2 MB | ||
| EGAF00006211239 | bai | 13.8 MB | ||
| EGAF00006211240 | bai | 13.9 MB | ||
| EGAF00006211241 | bai | 13.8 MB | ||
| EGAF00006211242 | bai | 6.5 MB | ||
| EGAF00006211243 | bai | 7.0 MB | ||
| EGAF00006211244 | bai | 5.9 MB | ||
| EGAF00006211245 | bai | 5.9 MB | ||
| EGAF00006211246 | bai | 4.7 MB | ||
| EGAF00006211247 | bai | 6.3 MB | ||
| 30 Files (263.9 GB) | ||||