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Sample_Manifest.Rmd
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Sample_Manifest.Rmd
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---
title: "Sample Manifest"
output: html_notebook
---
List of file ID's and names for each project
# Project P180312 (62GB)
Zcwpw1-HA & (h/c)Prdm9-V5 Co-transfections
- WTCHG_538916_217108 Sample:Input_ZCWPW1-HA Count:61279859
- WTCHG_538916_221156 Sample:ChIPHA_ZCWPW1-HA Count:65459828
- WTCHG_538916_220144 Sample:Input_ZCWPW1-HA+hPRDM9-V5 Count:67107524
- WTCHG_538916_223180 Sample:ChIPHA_ZCWPW1-HA+hPRDM9-V5 Count:66894286
- WTCHG_538916_224192 Sample:ChIPHA_ZCWPW1-HA+cPRDM9-V5 Count:62310491
```{bash}
wget -r ftp://baquifta:pouma-motru-36@bsg-ftp.well.ox.ac.uk/180629_K00150_0342_AHVYHYBBXX
md5sum -c P180312-md5sum.txt > P180312-md5sumCHECK.txt
```
# Project P180586 (57GB)
InVivo Chip against Zcwpw1 in Hybrid Mice
- WTCHG_594404_276139 Sample:Input_PWDB6F1 Count:75761495
- WTCHG_594404_277151 Sample:ChIPZCWPW1_PWDB6F1 Count:55372208
- WTCHG_594404_278163 Sample:Input_PWDB6humF1 Count:100880333
- WTCHG_594404_279175 Sample:ChIPZCWPW1_PWDB6humF1 Count:49620935
```{bash}
wget -r ftp://aifojhoo:kavfi-hethu-03@bsg-ftp.well.ox.ac.uk/181018_K00198_0357_BHWV5YBBXX
md5sum -c P180586-md5sum.txt > P180586-md5sumCHECK.txt
```
# Project P180717 (61GB)
ZFonlyPrdm9 cotransfections
Cotransfections with H3K4me3 (c/h)
ZfonlyPrdm9 only
- WTCHG_659233_233110 Sample:Input_ZCWPW1-HA+hPRDM9-ZFonly-V5 Count:24871157
- WTCHG_659233_234122 Sample:ChIPHA_ZCWPW1-HA+hPRDM9-ZFonly-V5 Count:22347286
- WTCHG_659233_235134 Sample:ChIPH3K4me3_ZCWPW1-HA+hPRDM9-ZFonly-V5 Count:25369086
- WTCHG_659233_249112 Sample:Input_ZCWPW1-HA+hPRDM9-V5 Count:30499498
- WTCHG_659233_250124 Sample:ChIPHA_ZCWPW1-HA+hPRDM9-V5 Count:27818259
- WTCHG_659233_251136 Sample:ChIPH3K4me3_ZCWPW1-HA+hPRDM9-V5 Count:25895561
- WTCHG_659233_252148 Sample:Input_ZCWPW1-HA+cPRDM9-V5 Count:29613874
- WTCHG_659233_253160 Sample:ChIPHA_ZCWPW1-HA+cPRDM9-V5 Count:26200675
- WTCHG_659233_254172 Sample:ChIPH3K4me3_ZCWPW1-HA+cPRDM9-V5 Count:25669210
- WTCHG_659233_255184 Sample:Input_hPRDM9-ZFonly-V5 Count:27442139
- WTCHG_659233_256196 Sample:ChIPV5_hPRDM9-ZFonly-V5 Count:29978613
```{r}
wget -r ftp://meigakuj:rygri-sekgo-36@bsg-ftp.well.ox.ac.uk/190301_K00181_0120_BH3NTJBBXY
cd bsg-ftp.well.ox.ac.uk/190301_K00181_0120_BH3NTJBBXY/
md5sum -c P180717-md5sum.txt > P180717-md5sumCHECK.txt
```
# Project P190297 (16GB)
Dmc1 ChipSeq
- WTCHG_688471 Sample:ZCW2.1ahomKO Count:35316203 Index 27
- WTCHG_688472 Sample:ZCW2.1bhetKO Count:55686978 Index 22
```{r}
wget -r ftp://citnocja:oagew-ijodo-63@bsg-ftp.well.ox.ac.uk/190524_D00529_0716_AH2G53BCX3
cd bsg-ftp.well.ox.ac.uk/190524_D00529_0716_AH2G53BCX3/
md5sum -c P190297-md5sum.txt > P190297-md5sumCHECK.txt
```
# Project P190297 (38GB)
Dmc1 ChipSeq pt2
- WTCHG_692839 Sample:ZCW2.1ahomKO_replacement Count:112,012,389 (AD022 = X (22,254,262), AD027 = HomKO (60,145,785))
- WTCHG_692840 Sample:ZCW2.1cWT Count:85,870,274 Index 09 (76,036,061)
```{r}
cd saxony/zcwpw1/raw_data/
wget -r ftp://citnocja:oagew-ijodo-63@bsg-ftp.well.ox.ac.uk/190621_D00529_0723_BH2WNHBCX3
cd bsg-ftp.well.ox.ac.uk/190621_D00529_0723_BH2WNHBCX3/
md5sum -c P190297-md5sum.txt > P190297-md5sumCHECK.txt
```
# Project P190456 (223 GB)
WGS
Project P190456 (223GB)
- WTCHG_706597_73135289 Sample:ZCW2.1a_HomKO Count:294815507
- WTCHG_706597_73145290 Sample:ZCW2.1c_WT Count:308589826
- WTCHG_706597_73155291 Sample:ZCW2.1b_HetKO Count:295197911
```{r}
cd saxony/zcwpw1/raw_data/
wget -r ftp://meivmang:edpai-rayps-00@bsg-ftp.well.ox.ac.uk/190814_A00711_0053_AHJWTWDSXX
cd bsg-ftp.well.ox.ac.uk/190814_A00711_0053_AHJWTWDSXX/
md5sum -c P190456-md5sum.txt > P190456-md5sumCHECK.txt
```
# Altemose2015
Remapping the data from Altemose et al 2015 (eLife) from hg37 to hg38
```{r}
#SRR5627143 ChIPseq.HumanPRDM9_HA.Input.ProtocolC
#SRR5627146 ChIPseq.HumanPRDM9_HA.antiHA.ProtocolC
#SRR5627144 ChIPseq.ChimpPRDM9_HA.antiHA.ProtocolC
#SRR5627145 ChIPseq.ChimpPRDM9_V5.antiV5.ProtocolC
#SRR5627147 ChIPseq.HumanPRDM9_V5.antiV5.ProtocolC
#SRR5627149 ChIPseq.HumanPRDM9_HA.antiH3K36me3.ProtocolC
#SRR5627152 ChIPseq.HumanPRDM9_HA.antiH3K4me3.ProtocolC.Rep1
#SRR5627153 ChIPseq.HumanPRDM9_HA.antiH3K4me3.ProtocolC.Rep2
#SRR5627142 ChIPseq.Untransfected.Input.ProtocolC
#SRR5627150 ChIPseq.Untransfected.antiH3K4me3.Rep1.ProtocolC
#SRR5627151 ChIPseq.Untransfected.antiH3K4me3.Rep2.ProtocolC
#SRR5627148 ChIPseq.Untransfected.antiH3K36me3.ProtocolC
#SRR5627140 ChIPseq.YFP_HumanPRDM9.Input.ProtocolN
#SRR5627138 ChIPseq.YFP_HumanPRDM9.antiGFP.Rep1.ProtocolN;
#SRR5627139 ChIPseq.YFP_HumanPRDM9.antiGFP.Rep2.ProtocolN
#SRR5627141 ChIPseq.YFP_HumanPRDM9.antiH3K4me3.ProtocolN
# https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99407
cd /homes/wells/saxony/zcwpw1/raw_data/altemose
# ChIPseq.ChimpPRDM9_V5.antiV5.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/005/SRR5627145/SRR5627145_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/005/SRR5627145/SRR5627145_2.fastq.gz
# ChIPseq.HumanPRDM9_V5.antiV5.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/007/SRR5627147/SRR5627147_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/007/SRR5627147/SRR5627147_2.fastq.gz
# ChIPseq.HumanPRDM9_HA.Input.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/003/SRR5627143/SRR5627143_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/003/SRR5627143/SRR5627143_2.fastq.gz
# ChIPseq.HumanPRDM9_HA.antiHA.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/006/SRR5627146/SRR5627146_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/006/SRR5627146/SRR5627146_2.fastq.gz
# ChIPseq.ChimpPRDM9_HA.antiHA.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/004/SRR5627144/SRR5627144_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/004/SRR5627144/SRR5627144_2.fastq.gz
# ChIPseq.HumanPRDM9_HA.antiH3K36me3.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/009/SRR5627149/SRR5627149_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/009/SRR5627149/SRR5627149_2.fastq.gz
# ChIPseq.HumanPRDM9_HA.antiH3K4me3.ProtocolC.Rep1
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/002/SRR5627152/SRR5627152_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/002/SRR5627152/SRR5627152_2.fastq.gz
# ChIPseq.HumanPRDM9_HA.antiH3K4me3.ProtocolC.Rep2
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/003/SRR5627153/SRR5627153_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/003/SRR5627153/SRR5627153_2.fastq.gz
# ChIPseq.Untransfected.Input.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/002/SRR5627142/SRR5627142_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/002/SRR5627142/SRR5627142_2.fastq.gz
# ChIPseq.Untransfected.antiH3K4me3.Rep1.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/000/SRR5627150/SRR5627150_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/000/SRR5627150/SRR5627150_2.fastq.gz
# ChIPseq.Untransfected.antiH3K4me3.Rep2.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/001/SRR5627151/SRR5627151_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/001/SRR5627151/SRR5627151_2.fastq.gz
# ChIPseq.Untransfected.antiH3K36me3.ProtocolC
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/008/SRR5627148/SRR5627148_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/008/SRR5627148/SRR5627148_2.fastq.gz
#ChIPseq.YFP_HumanPRDM9.antiGFP.Rep1.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/008/SRR5627138/SRR5627138_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/008/SRR5627138/SRR5627138_2.fastq.gz
#ChIPseq.YFP_HumanPRDM9.antiGFP.Rep2.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/009/SRR5627139/SRR5627139_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/009/SRR5627139/SRR5627139_2.fastq.gz
#ChIPseq.YFP_HumanPRDM9.Input.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/000/SRR5627140/SRR5627140_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/000/SRR5627140/SRR5627140_2.fastq.gz
#ChIPseq.YFP_HumanPRDM9.antiH3K4me3.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/001/SRR5627141/SRR5627141_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/001/SRR5627141/SRR5627141_2.fastq.gz
#ChIPseq.Untransfected.Input.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/007/SRR5627137/SRR5627137_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/007/SRR5627137/SRR5627137_2.fastq.gz
#ChIPseq.Untransfected.antiH3K4me3.Rep2.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/006/SRR5627136/SRR5627136_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/006/SRR5627136/SRR5627136_2.fastq.gz
#ChIPseq.Untransfected.antiH3K4me3.Rep1.ProtocolN
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/005/SRR5627135/SRR5627135_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR562/005/SRR5627135/SRR5627135_2.fastq.gz
for FILENAME in SRR*; do mv $FILENAME SRA_Altemose2015_$FILENAME; done
#cd /homes/wells/saxony/single-cell/sequencing/zcwpwp1/
cd /homes/wells/saxony/zcwpw1/
```