Hi, I'm an undergraduate student. Please help me.

I want mapping-bam-file from sra-dataset from NCBI in order to analyze heterogeneity of mouse ESC.

The dataset is generated from a paper below.(GSE60749)

*Roshan M.Kumar et al. Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature(2014)*

Please teach me how to get adapter sequence used in this experimentation

and what I should use for quality control(Prinseq?ShortRead?).

For example, I want to try GEO Sample [GSM1486817][1] sra file.

Can anyone give me process of quality control of this sra?

I thank you for reading it through.

Any help will be appreciated.

 [1]: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1486817
1. Download data
2. Convert from` .sra `format to .`fastq` with **SRA Toolkit**: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
3. Check the quality using **fastQC** package: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. In the generated report, you will see if your sequences have adapters and if so, their names.
4. Remove the adapters and bad quality sequences using:
   - **Trimmomatic**: http://www.usadellab.org/cms/?page=trimmomatic
   - **AdapterRemoval**: https://github.com/mikkelschubert/adapterremoval
   - **Cutadapt**: http://journal.embnet.org/index.php/embnetjournal/article/view/200/479
   - ... and many other tools. I would suggest you Trimmomatic.

These are the general steps that you should follow in order to perform a quality control of the raw data.

Hope it helps.