... | ... | @@ -51,7 +51,19 @@ For full description of the sample preparation protocol and pre-processing of se |
|
|
---
|
|
|
### **Data Characteristics** <br>
|
|
|
Post sequencing, transcript structures were defined by applying the isoform-level clustering algorithm ([ICE](https://github.com/PacificBiosciences/cDNA_primer/wiki)) on full-length reads, capturing the entire mRNA molecule (containing 5', polyA-tail and 3' primer sequences). To find transcript clusters, ICE performs a pairwise alignment and reiterative assignment of full-length reads to clusters based on likelihood. This process is followed by consensus calling and further polishing of the sequence to reduce redundancy and increase the overall accuracy of sequences for identified transcript variants. Our analysis pipeline could precisely determine the position of polyadenylation site (presence of polyA-tail) and intro-exon boundaries, as evident from the presence of the canonical **GU** motif in 93% of donor splice sites and the canonical **AG** motif in 95% of acceptor splice sites. In addition to 7,364 single-exon transcripts, the MCF-7 transcriptome consists of 11,350 multi-exon genes of which 69% produced multiple transcript structures (**Figure 1**; [GFF](); [FASTA]()). Furthermore, 49% of identified transcripts in MCF-7 cells are potentially novel in comparison with the [GENCODE](http://www.gencodegenes.org/) annotation (versoin 19). The comparison was carried out using `cuffcompare` from Cufflinks suite. <br>
|
|
|
<br>
|
|
|
<br>
|
|
|
|
|
|
<br>
|
|
|
> **Figure 1:** Overview of identified transcripts in MCF-7 transcriptome. Histograms show the distribution of the number of identified transcripts per gene and transcript lengths. Density plot depicts the number of supporting reads based on transcript length. The number of supporting reads does not correlate with the length of full-length transcripts.
|
|
|
|
|
|
|
|
|
<br>
|
|
|
|
|
|
---
|
|
|
### **Prerequisites** <br> |
|
|
\ No newline at end of file |
|
|
### **Prerequisites** <br>
|
|
|
|
|
|
This is the script used for this task: <br>
|
|
|
```python
|
|
|
for i in range(0,10):
|
|
|
print 'hellow'
|
|
|
``` |
|
|
\ No newline at end of file |