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
<p>You can find the adapters used by reading a bit and googling around. &quot;Nextera XT DNA Sample preparation reagents (Illumina)&quot; were used to prepare the samples (as found <a href="http://www.ncbi.nlm.nih.gov/sra?term=SRX686234">here</a> under &quot;study summary&quot;, or <a href="http://www.ncbi.nlm.nih.gov/sra/SRX686234/">here</a> under &quot;library&quot;).</p>

<p>You can check for adapter contamination with <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a>.</p>

<p><strong>edit:</strong> if the downstream analysis to be performed is mapping with BWA, Bowtie2 or any mapper which performs local alignment, adapter should not have a major impact. Besides, the reads he pointed to in his question are 25+25, which should be shorter than Nextera typical insert size, and adapter contamination should be really low.</p>
