rna-seq-pipeline
需积分: 9 111 浏览量
2021-05-08
15:27:01
上传
评论
收藏 254.41MB ZIP 举报
rna-seq-pipeline-master.zip （87个子文件） 
rna-seq-pipeline-master 
.dockerignore 40B .flake8 40B output_definition.json 10KB workflow_opts docker.json 312B singularity.json 115B rna-seq-pipeline.wdl 11KB
test_env_requirements.txt 52B src prep_star.sh 2KB prep_rsem.sh 2KB mad_qc.py 2KB __init__.py 0B merge_annotation.py 4KB align.py 11KB rna_qc.py 4KB test test_align.py 3KB test_rna_qc.py 3KB test_rsem_quant.py 1KB test_compare_md5.py 2KB __init__.py 0B test_merge_annotation.py 3KB MAD.R 2KB prep_kallisto.sh 146B kallisto_quant.py 9KB prep_srna.sh 1KB bam_to_signals.py 4KB rsem_quant.py 4KB compare_md5.py 4KB transcript_id_to_gene_type_mappings gencodeV29pri-UCSC-tRNAs-ERCC-phiX.transcript_id_to_genes.tsv 6.51MB gencodeV24pri-tRNAs-ERCC-phiX.transcript_id_to_genes.tsv 6.22MB gencodeM21pri-UCSC-tRNAs-ERCC-phiX.transcript_id_to_genes.tsv 5.27MB Dockerfile 2KB .circleci config.yml 9KB annotations_and_spikeins 
gencode.v19.tRNAs.gtf.gz 13KB gencode.v19.annotation.gtf.gz 35.34MB gencode.vM7.tRNAs.gtf.gz 543KB ENCFF824ZKD_gencodeV24pri-tRNAs-ERCC-phiX.gtf.gz 39.53MB gencode.vM7.annotation.gtf.gz 22.31MB ENCFF001RTP_spikes_ENCFF335FFV_spikes.fasta.gz 29KB gencode.vM7.trna.ercc.phix.gtf.gz 22.84MB ENCFF871VGR_gencodeM21pri-UCSC-tRNAs-ERCC-phiX.gtf.gz 26.23MB ENCFF159KBI_gencodeV29pri-UCSC-tRNAs-ERCC-phiX.gtf.gz 37.6MB gencode.v19.trna.ercc.phix.gtf.gz 35.37MB make_index_wdl build_genome_index.wdl 2KB merge_anno.wdl 1KB .isort.cfg 193B LICENSE 1KB test cromwell_options.json 153B test_task test_align_PE_input.json 643B test_align_SE_input.json 649B test_align_PE_reference_md5.json 151B test_align_SE_reference_md5.json 299B test_align.wdl 785B test_workflow PE_stranded_reference_md5.json 1KB PE_stranded_input.json 1KB SE_unstranded_input.json 1KB PE_unstranded_input.json 1KB PE_unstranded_reference_md5.json 540B SE_unstranded_reference_md5.json 1KB caper_run.sh 404B README.md 1KB .pre-commit-config.yaml 709B test_data rep1_ENCSR510QZW_chr19only_10000_reads_part2.fastq.gz 291KB ERCC_phiX.fa.gz 29KB ENCSR653DFZ_rep1_chr19_10000reads_R1.fastq.gz 863KB GRCh38_no_alt_analysis_set_GCA_000001405.15_onlychr19.fa.gz 15.51MB rep1_ENCSR510QZW_chr19only_10000_reads.fastq.gz 590KB ENCSR653DFZ_rep2_chr19_10000reads_R2.fastq.gz 854KB rep1_ENCSR510QZW_chr19only_10000_reads_part1.fastq.gz 300KB ENCSR142YZV_chr19only_10000_reads_R2.fastq.gz 700KB ENCSR142YZV_chr19only_10000_reads_R1.fastq.gz 584KB ENCSR142YZV_chr19only_10000_reads_R1_part1.fastq.gz 298KB ENCSR653DFZ_rep2_chr19_10000reads_R1.fastq.gz 867KB GRCh38_EBV.chrom.sizes 11KB ENCSR142YZV_chr19only_10000_reads_R2_part1.fastq.gz 355KB rep2_ENCSR510QZW_chr19only_10000_reads_part1.fastq.gz 313KB gencodeV24pri-tRNAs-ERCC-phiX_onlychr19_and_spikeins.gtf.gz 2.33MB Homo_sapiens.GRCh38.cdna.all.chr19_ERCC_phix.fa.gz 3.31MB ENCSR142YZV_chr19only_10000_reads_R2_part2.fastq.gz 345KB ENCSR653DFZ_rep1_chr19_10000reads_R2.fastq.gz 847KB GRCh38_v24_ERCC_phiX_rsemIndex_chr19only.tgz 10.13MB rep2_ENCSR510QZW_chr19only_10000_reads.fastq.gz 617KB rep2_ENCSR510QZW_chr19only_10000_reads_part2.fastq.gz 304KB ENCSR142YZV_chr19only_10000_reads_R1_part2.fastq.gz 287KB docs howto.md 10KB installation.md 3KB reference.md 21KB .gitignore 1KB资源评论
