Readme.md

Data

Raw Data

raw source data

given 6 samples, download-scripts provided:

• https://www.ebi.ac.uk/ena/browser/view/SRX2837380
• https://www.ebi.ac.uk/ena/browser/view/SRX2837381
• https://www.ebi.ac.uk/ena/browser/view/SRX2837378
• https://www.ebi.ac.uk/ena/browser/view/SRX2837379
• https://www.ebi.ac.uk/ena/browser/view/SRX2837376
• https://www.ebi.ac.uk/ena/browser/view/SRX2837377

tree -I '*.sh|dm6.fa' TADs_data_zipped

TADs_data_zipped
├── SRX2837376-fastq_ftp-20231214-0515
│  ├── SRR5579160.fastq.gz
│  ├── SRR5579160_1.fastq.gz
│  ├── SRR5579160_2.fastq.gz
│  ├── SRR5579161.fastq.gz
│  ├── SRR5579162.fastq.gz
│  ├── SRR5579162_1.fastq.gz
│  ├── SRR5579162_2.fastq.gz
│  ├── SRR5579163.fastq.gz
│  ├── SRR5579163_1.fastq.gz
│  ├── SRR5579163_2.fastq.gz
│  ├── SRR5579164.fastq.gz
│  ├── SRR5579164_1.fastq.gz
│  ├── SRR5579164_2.fastq.gz
│  ├── SRR5579165.fastq.gz
│  ├── SRR5579165_1.fastq.gz
│  ├── SRR5579165_2.fastq.gz
│  ├── SRR5579166.fastq.gz
│  ├── SRR5579166_1.fastq.gz
│  └── SRR5579166_2.fastq.gz
├── SRX2837377-fastq_ftp-20231214-0516
│  ├── SRR5579167_1.fastq.gz
│  ├── SRR5579167_2.fastq.gz
│  ├── SRR5579168_1.fastq.gz
│  ├── SRR5579168_2.fastq.gz
│  ├── SRR5579169_1.fastq.gz
│  └── SRR5579169_2.fastq.gz
├── SRX2837378-fastq_ftp-20231214-0514
│  ├── SRR5579170_1.fastq.gz
│  ├── SRR5579170_2.fastq.gz
│  ├── SRR5579171_1.fastq.gz
│  ├── SRR5579171_2.fastq.gz
│  ├── SRR5579172_1.fastq.gz
│  ├── SRR5579172_2.fastq.gz
│  ├── SRR5579173_1.fastq.gz
│  └── SRR5579173_2.fastq.gz
├── SRX2837379-fastq_ftp-20231214-0514
│  ├── SRR5579174_1.fastq.gz
│  ├── SRR5579174_2.fastq.gz
│  ├── SRR5579175_1.fastq.gz
│  ├── SRR5579175_2.fastq.gz
│  ├── SRR5579176_1.fastq.gz
│  └── SRR5579176_2.fastq.gz
├── SRX2837380-fastq_ftp-20231214-0425
│  ├── SRR5579177_1.fastq.gz
│  └── SRR5579177_2.fastq.gz
└── SRX2837381-fastq_ftp-20231214-0513
   ├── SRR5579178_1.fastq.gz
   └── SRR5579178_2.fastq.gz

reference genome

fruit fly reference genome (latest: dm6)

• https://hgdownload.soe.ucsc.edu/downloads.html#fruitfly

dm6.fa.gz - "Soft-masked" assembly sequence in one file. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.

Processed Data

genome index

You may build genome index with bowtie2 or bwa.

In our case, we use bowtie2 to build genome index. (this is assumed you have bowtie2 installed)

bowtie2-build dm6.fa dm6

dm6.1.bt2
dm6.2.bt2
dm6.3.bt2
dm6.4.bt2
dm6.rev.1.bt2
dm6.rev.2.bt2