Create workflows of next generation sequencing by Galaxy system or R. Perform QC

Question

Create workflows of next generation sequencing by Galaxy system or R.

Perform QC analysis of RNA-SEQ NGS dataset using FASTQC

Map next generation sequence dataset using BWA-MEM (application)

Produce statistics for BAM dataset by SAMTools Stats

Develop a workflow for Variant Calling (creating a VCF file) and Annotate by program available in Galaxy

The compulsory for the assignment are to provide information to reproduce the analysis. The work you did should be written for reproduction by another person.

Here is something needed to show how the above analysis can be reproduced;

A written explanation of the analysis completed as well as programs, modules and data formats

Identifiers for the datasets and their source

Statistics around created BAM file

Figure of workflow steps for the analysis you completed

Figure of workflow steps used to conduct variant analysis

A written report of the variant workflow as well as recognizing programs used and data formats used

Challenges come across and suggestions to improve the project

Explanation / Answer

We all knew that Quality Control (QC) is very critical in term of RNA sequencing. And this QC can be performed using FASTQC.

We have done the QC analysis of RNA-SEQ NGS dataset using FASTQC with default setting and after that we got a report. According to the report our analysis is as follows:

1) The integiry of RNA is maintained which means we can obtain quality data from it.
2) We have also observed the following parameters and all are in good conditions:
   1) Total numbers of read sequenced.
   2) GC content
   3) base quality score
3) We also observed the distribution of MAPQ and it is Ok. So we can say that overall alignment quality is good.

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