To be able to fully re-analyze the data, please the full TERA-Seq dataset from SRA BioProject accession: PRJNA673166, put the downloaded fastq.gz files to directories names by Library name/fastq (please see the table bellow) in this directory and rename the downloaded fastq.gz files to reads.1.fastq.gz.
For example, the prepared Cap-Poly(A) fastq.gz have to be placed in hsa.dRNASeq.HeLa.polyA.CIP.decap.REL5.long.1/fastq/reads.1.fastq.gz in this directory. The analysis will not work without the samples directory populated exactly this way!
For basecalling and analysis of poly(A) tail lengths you need to download the corresponding fast5 files and place them in fast5 directory for each of the libraries. Please note the provided fast5 files are already basecalled (Guppy 3.3.2-1). Please note the basecalling was run without RTA trimming. For more details on basecalling please see run_Guppy.sh.
After you prepared the input samples/files you can run run.sh script to process the sample files.
| Library type | Sample name | fast5 | fast5 md5 | fastq | SRA | Library name |
|---|---|---|---|---|---|---|
| 5TERA | Cap-Poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.CIP.decap.REL5.long.1 |
| 5TERA | Cap & 5P-Poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.decap.REL5.long.1 |
| 5TERA | 5P-Poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.REL5.long.1 |
| 5TERA | 5OH-Poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.REL5OH.long.1 |
| 5TERA-short | 5P short-Poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.REL5.1 |
| 5TERA-short | 5 short-PNK-Poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.PNK.REL5.1 |
| TERA3 | TERA3_replicate1 | download | download | download | link | hsa.dRNASeq.HeLa.total.REL3.1 |
| TERA3 | TERA3_replicate2 | download | download | download | link | hsa.dRNASeq.HeLa.total.REL3.2 |
| TERA3 | TERA3_replicate3 | download | download | download | link | hsa.dRNASeq.HeLa.total.REL3.3 |
| 5TERA3 | 5TERA3_replicate1 | download | download | download | link | hsa.dRNASeq.HeLa.total.REL5.long.REL3.4 |
| 5TERA3 | 5TERA3_replicate2 | download | download | download | link | hsa.dRNASeq.HeLa.total.REL5.long.REL3.5 |
| 5TERA3 | 5TERA3_replicate3 | download | download | download | link | hsa.dRNASeq.HeLa.total.REL5.long.REL3.6 |
| Standard dRNA | CTRL-poly(A) | download | download | download | link | hsa.dRNASeq.HeLa.polyA.1 |
To re-analyze analysis using external data please populate the additional directories. Follow the same instructions as for TERA-Seq using the table bellow.
| Library type | Sample name | fastq | SRA | Library name |
|---|---|---|---|---|
| Mouse SIRV | SIRV_replicate1 | download | link | mmu.dRNASeq.inclSIRV.PRJEB27590.ERR2680375.1 |
| Mouse SIRV | SIRV_replicate2 | download | link | mmu.dRNASeq.inclSIRV.PRJEB27590.ERR2680379.1 |
| Mouse SIRV | SIRV_replicate3 | download | link | mmu.dRNASeq.inclSIRV.PRJEB27590.ERR3363657.1 |
| Mouse SIRV | SIRV_replicate4 | download | link | mmu.dRNASeq.inclSIRV.PRJEB27590.ERR3363659.1 |
| RNASeq | Illumina (RNA-Seq) | download, download | link, ENCODE | hsa.RNASeq.HeLa.xxx.polyA.ENCSR000CPR.1 |
| RiboSeq | Ribo-Seq | download | link | hsa.RiboSeq.HeLa.async.2 |
| Akron5Seq | Akron5 | download, download | link | hsa.Akron5Seq.HeLa.whole.2 |
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