# seqcii-hcc1395: full-size HCC1395 WGTS test data Full-size Illumina FASTQ test data for the `wgts` workflow of [nf-core/oncoanalyser](https://nf-co.re/oncoanalyser). Represents a typical tumour/normal sample at ~40x normal WGS, ~80x tumour WGS, and ~5x tumour WTS. Reads are split across multiple FASTQ files for convenient parallelisation of alignment. ## Source data | Sample | Library | BioSample | SRA experiment | SRA run(s) | Platform | Study | |- |- |- |- |- |- |- | | Normal WGS | WGS_IL_N_1 | SAMN10102574 | SRX4728509 | SRR7890859, SRR7945633, SRR7945634, SRR7945663 | Illumina HiSeq 4000 | SEQC2 (PRJNA489865) | | Tumour WGS | WGS_IL_T_1 | SAMN10102573 | SRX4728512 | SRR7890856 | Illumina HiSeq 4000 | SEQC2 (PRJNA489865) | | Tumour WTS | 2891075264 | SAMN02146417 | SRX278519 | SRR892423 | Illumina HiSeq 2000 | WUGSC (PRJNA201238) | > The tumour WTS is matched from a different study (PRJNA201238, the Washington University Genome Center HCC1395/HCC1395BL cell-line project) because SEQC2 does not provide bulk WTS. SEQC2 study accession: SRP162370. See the [SEQC2 portal](https://sites.google.com/view/seqc2). SRA runs were downloaded from the public SRA Open Data Program bucket (`s3://sra-pub-run-odp`). ## Downsampling The full-depth reads were subsampled with `seqtk sample` to reach the target coverages below. Coverage figures are ORANGE mean coverage from an independent oncoanalyser run of the full-depth reads. | Sample | Source | Target | Subsample fraction | |- |- |- |- | | Normal WGS | 84.6x | 40x | 0.4728132388 | | Tumour WGS | 93.5x | 80x | 0.8556149733 | | Tumour WTS | ~13x | ~5x | 0.3891767415 | ## Process ### Download SRA files ```bash mkdir -p logs/ sample_ids='2891075264 SRR892423 WGS_IL_N_1 SRR7890859 WGS_IL_N_1 SRR7945633 WGS_IL_N_1 SRR7945634 WGS_IL_N_1 SRR7945663 WGS_IL_T_1 SRR7890856' parallel -j6 --colsep ' ' 'aws s3 cp --no-sign-request s3://sra-pub-run-odp/sra/{2}/{2} data/sra/{1}__{2}.sra 1>logs/sra_{1}__{2}.log.txt 2>&1' ::: "${sample_ids}" ``` ### Convert SRA files to FASTQ ```bash wget -P software/ https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.3.0/sratoolkit.3.3.0-ubuntu64.tar.gz (cd software/ && tar -zxvf sratoolkit.3.3.0-ubuntu64.tar.gz) find data/sra/ -type f -name '*.sra' | \ parallel -j2 './software/sratoolkit.3.3.0-ubuntu64/bin/fasterq-dump --progress {} --threads 2 --outdir data/fastq/ 1>logs/fastq_{/.}.log.txt 2>&1' ``` ### Compress ```bash for pi in $(find data/fastq/ -type f -name '*.fastq'); do echo ${pi}; pigz -p16 ${pi}; done ``` ### Subsample to target depths ```bash mkdir -p data/fastq_subsampled/ subsample_rates='''data/fastq/2891075264__SRR892423_1.fastq.gz 0.3891767415 data/fastq/2891075264__SRR892423_2.fastq.gz 0.3891767415 data/fastq/WGS_IL_N_1__SRR7890859_1.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7890859_2.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7945633_1.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7945633_2.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7945634_1.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7945634_2.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7945663_1.fastq.gz 0.4728132388 data/fastq/WGS_IL_N_1__SRR7945663_2.fastq.gz 0.4728132388 data/fastq/WGS_IL_T_1__SRR7890856_1.fastq.gz 0.8556149733 data/fastq/WGS_IL_T_1__SRR7890856_2.fastq.gz 0.8556149733''' parallel -j2 --colsep ' ' 'seqtk sample -s0 {1} {2} | pigz -c -p16 > {=1 s#/fastq/#/fastq_subsampled/#; s#_(..fastq.gz)#.subsampled.\1#=}' ::: "${subsample_rates}" ``` ### Split tumour WGS into 8 paired-end pairs ```bash mkdir -p data/fastq_subsampled_split/ fastp \ --in1 data/fastq_subsampled/WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz \ --in2 data/fastq_subsampled/WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz \ --disable_quality_filtering \ --disable_length_filtering \ --disable_adapter_trimming \ --disable_trim_poly_g \ --split_by_lines 460600000 \ --thread 8 \ --out1 data/fastq_subsampled_split/WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz \ --out2 data/fastq_subsampled_split/WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz ``` ### Rename to final names ```bash mkdir -p data/fastq_final/ fp_names=''' fastq_subsampled/2891075264__SRR892423.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wts__2891075264__SRR892423__subsampled.1.fastq.gz fastq_subsampled/2891075264__SRR892423.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wts__2891075264__SRR892423__subsampled.2.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7890859.subsampled.1.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7890859__subsampled.1.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7890859.subsampled.2.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7890859__subsampled.2.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7945633.subsampled.1.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7945633__subsampled.1.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7945633.subsampled.2.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7945633__subsampled.2.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7945634.subsampled.1.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7945634__subsampled.1.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7945634.subsampled.2.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7945634__subsampled.2.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7945663.subsampled.1.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7945663__subsampled.1.fastq.gz fastq_subsampled/WGS_IL_N_1__SRR7945663.subsampled.2.fastq.gz data/fastq_final/HCC1395__normal_wgs__WGS_IL_N_1__SRR7945663__subsampled.2.fastq.gz fastq_subsampled_split/0001.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_1.1.fastq.gz fastq_subsampled_split/0001.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_1.2.fastq.gz fastq_subsampled_split/0002.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_2.1.fastq.gz fastq_subsampled_split/0002.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_2.2.fastq.gz fastq_subsampled_split/0003.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_3.1.fastq.gz fastq_subsampled_split/0003.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_3.2.fastq.gz fastq_subsampled_split/0004.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_4.1.fastq.gz fastq_subsampled_split/0004.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_4.2.fastq.gz fastq_subsampled_split/0005.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_5.1.fastq.gz fastq_subsampled_split/0005.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_5.2.fastq.gz fastq_subsampled_split/0006.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_6.1.fastq.gz fastq_subsampled_split/0006.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_6.2.fastq.gz fastq_subsampled_split/0007.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_7.1.fastq.gz fastq_subsampled_split/0007.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_7.2.fastq.gz fastq_subsampled_split/0008.WGS_IL_T_1__SRR7890856.subsampled.1.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_8.1.fastq.gz fastq_subsampled_split/0008.WGS_IL_T_1__SRR7890856.subsampled.2.fastq.gz data/fastq_final/HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_8.2.fastq.gz ''' while read -a data; do if [[ ${data[@]} == "" ]]; then continue; fi; ln -s ../${data[0]} ${data[1]}; done <<< "${fp_names}" ``` ## Final files The dataset is 26 gzip-compressed FASTQ files. Naming is `HCC1395_________subsampled[__split_N].{1,2}.fastq.gz`. | File | Size (GiB) | |- |- | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7890859__subsampled.1.fastq.gz | 10.6 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7890859__subsampled.2.fastq.gz | 11.9 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7945633__subsampled.1.fastq.gz | 10.5 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7945633__subsampled.2.fastq.gz | 11.6 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7945634__subsampled.1.fastq.gz | 9.4 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7945634__subsampled.2.fastq.gz | 10.5 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7945663__subsampled.1.fastq.gz | 8.8 | | HCC1395__normal_wgs__WGS_IL_N_1__SRR7945663__subsampled.2.fastq.gz | 9.8 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_1.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_1.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_2.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_2.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_3.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_3.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_4.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_4.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_5.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_5.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_6.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_6.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_7.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_7.2.fastq.gz | 11.2 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_8.1.fastq.gz | 10.1 | | HCC1395__tumour_wgs__WGS_IL_T_1__SRR7890856__subsampled__split_8.2.fastq.gz | 11.2 | | HCC1395__tumour_wts__2891075264__SRR892423__subsampled.1.fastq.gz | 4.6 | | HCC1395__tumour_wts__2891075264__SRR892423__subsampled.2.fastq.gz | 4.6 | Total size: 262.5 GiB (281,866,489,692 bytes) across the 26 files. Normal WGS 83.1 GiB, tumour WGS 170.2 GiB, WTS 9.2 GiB. Each FASTQ has a corresponding `.sha256` hash file placed directly alongside the `.fastq.gz` files in the iGenomes bucket. After downloading, verify all 26 from the directory holding both the FASTQs and their hash files: ```bash parallel -j0 sha256sum -c ::: *.sha256 ``` ## Maintainer Stephen Watts