Skip to content

Commit 4067d6e

Browse files
owlangowlang
committed
setup BY4742 test of StrainID on real data
Using the Hsf1 ChIPseq data from de Jong et al 2017, we can test StrainID's ability to identify the BY4742 strain background. This commit includes the metadata and README updates including placeholders for results and log directories. SraRunInfo.csv pulled from NCBI SRA search.
1 parent 908adc3 commit 4067d6e

5 files changed

Lines changed: 32 additions & 1 deletion

File tree

‎paper/BY4742-chipseq/README‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
# Run StrainID on BY4742 datasets to evaluate StrainID's ability to detect the variant-based strain background
2+
3+
# "Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters"
4+
# (de Jonge et al, 2017)
5+
6+
# GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81787
7+
8+
# The default sacCer3 StrainID database is used
9+
# Download data using SRA accessions using `job/00_download_data.pbs`
10+
# Align FASTQ files and process using `job/01_align_data.pbs`
11+
# Run StrainID on BAM inputs using `job/02_run_StrainID.pbs` to determine if StrainID can successfully identify the strain background
12+
13+
#specifically look into performance in distinguishing two closesly related strains: BY4741 and BY4742

‎paper/BY4742-chipseq/SraRunInfo.csv‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
2+
SRR3497399,2017-05-11 00:00:55,2016-05-11 11:04:54,67640691,3281838684,0,48,1816,GCF_000146045.2,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3497399/SRR3497399.1,SRX1756249,Hsf1_ChIP,ChIP-Seq,ChIP,GENOMIC,SINGLE,0,0,ABI_SOLID,AB 5500xl-W Genetic Analysis System,SRP074822,PRJNA321111,,321111,SRS1432863,SAMN04966256,simple,4932,Saccharomyces cerevisiae,Hsf1_ChIP,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,F73F96964C383156F61A669AC0074AD9,443BEFEC858B5AF9C065249419528A69
3+
SRR3497410,2017-05-11 00:00:55,2016-05-11 11:08:21,80694279,3905823162,0,48,2028,GCF_000146045.2,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-7/SRR3497410/SRR3497410.1,SRX1756250,Hsf1_input,ChIP-Seq,unspecified,GENOMIC,SINGLE,0,0,ABI_SOLID,AB 5500xl-W Genetic Analysis System,SRP074822,PRJNA321111,,321111,SRS1432864,SAMN04966257,simple,4932,Saccharomyces cerevisiae,Hsf1_input,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,C76260FC0AED0743E40E038EEC232960,D96A93109D0C695D8263594CD89E9473
4+
SRR3497446,2017-05-11 00:00:55,2016-05-17 11:46:57,56996253,8537022864,56996253,149,3350,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497446/SRR3497446.1,SRX1756259,Hsf1_t0_0.05U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432872,SAMN04966258,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_0.05U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,1D79B28E58E73793E3F2416BE52FC99B,A4C02F8943A763A0C413FF046BA716B5
5+
SRR3497452,2017-05-11 00:00:56,2016-05-11 11:24:59,62257597,9364630504,62257597,150,3611,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497452/SRR3497452.1,SRX1756270,Hsf1_t0_0.2U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432882,SAMN04966260,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_0.2U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,103A6282A4032934D6050C6DD2B5E6BF,871F9BAEC203D09E57EB5726F7A84CD1
6+
SRR3497453,2017-05-11 00:00:56,2016-05-11 12:06:21,61425579,9217294875,61425579,150,3523,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497453/SRR3497453.1,SRX1756274,Hsf1_t0_0.8U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432886,SAMN04966262,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_0.8U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,851EA8BF587B0C7F08802CD998CA5246,5BDD7B50B89F79F3CEC01DA4ABA31660
7+
SRR3497454,2017-05-11 00:00:56,2016-05-11 12:01:49,48284496,7235073133,48284496,149,2828,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497454/SRR3497454.1,SRX1756275,Hsf1_t0_3.0U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432887,SAMN04966264,simple,4932,Saccharomyces cerevisiae,Hsf1_t0_3.0U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,220B1999B9CB4227F5A35B51BCC72724,2F01C0E9269BD0FA1523461BC01D8198
8+
SRR3497449,2017-05-11 00:00:56,2016-05-11 13:19:10,53608235,8028655564,53608235,149,3153,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497449/SRR3497449.1,SRX1756263,Hsf1_t30_0.05U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432875,SAMN04966259,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_0.05U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,A5A12C5FFFE69D3ABB4F0C42AE0FF7EA,5D151CA79CC01ACCE3C98CF5E646DD47
9+
SRR3497456,2017-05-11 00:00:56,2016-05-11 14:19:38,62404674,9388451136,62404674,150,3646,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-8/SRR3497456/SRR3497456.1,SRX1756283,Hsf1_t30_0.2U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432895,SAMN04966261,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_0.2U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,4D316816A01301B7B30F9CC1381B5018,DDDB3A1D0A7A3F6255418B0C27D316E6
10+
SRR3497459,2017-05-11 00:00:56,2016-05-11 14:21:03,70846857,10638854137,70846857,150,4074,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos2/sra-pub-run-3/SRR3497459/SRR3497459.1,SRX1756286,Hsf1_t30_0.8U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432898,SAMN04966263,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_0.8U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,9C84D57EE58BF1B09AF37E3504851620,C6850B43795D5AF9504DF7A5F4625B13
11+
SRR3497461,2017-05-11 00:00:56,2016-05-11 15:19:34,52591831,7857035482,52591831,149,3032,,https://sra-downloadb.st-va.ncbi.nlm.nih.gov/sos1/sra-pub-run-8/SRR3497461/SRR3497461.1,SRX1756287,Hsf1_t30_3.0U,MNase-Seq,MNase,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP074822,PRJNA321111,,321111,SRS1432899,SAMN04966265,simple,4932,Saccharomyces cerevisiae,Hsf1_t30_3.0U,,,,,,,no,,,,,PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY,SRA424700,,public,00F78D41D1508EDEFAC4DE473028A626,6EB7361E2E83CF786951734E6596C8F0
12+

‎paper/BY4742-chipseq/logs/README‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
# logfiles from STDERR and STDOUT of running job files go here

‎paper/BY4742-chipseq/results/README‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
# Downloaded FASTQ files and StrainID results go here

‎paper/README‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@ paper
1616
|--ENCODEdata-CellLines
1717
|--HIV_samples
1818
|--YKOC-wgs
19+
|--BY4742-chipseq
1920
|--CENPK-chipseq
2021

2122

@@ -55,5 +56,8 @@ contains the scripts and information for downloading, processing, and running Ep
5556
## YKOC-wgs
5657
contains the scripts and information for downloading, processing, and running DeletionID on the Puddu et al, 2019 dataset for identifying deletions
5758

59+
## BY4742-chipseq
60+
contains the scripts and information for downloading, processing, and running StrainID on the BAM files
61+
5862
## CENPK-chipseq
59-
contains the scripts and information for downloading, processing, and running StrainID on the
63+
contains the scripts and information for downloading, processing, and running StrainID on the BAM files

0 commit comments

Comments
 (0)