Edgen RNAseq - Revision history

Rf at 21:47, 25 May 2016

2016-05-25T21:47:27Z

2016-05-25T21:21:45Z

2016-05-25T21:08:45Z

2016-05-22T22:17:10Z

Created page with "= Introduction = This is based on Edinburgh Genomics' two day RNAseq course. = Steps in Brief ="

New page

= Introduction =

This is based on Edinburgh Genomics' two day RNAseq course.

= Steps in Brief =

@@ Line 22: / Line 22: @@
   java -jar $PICARD/MarkDuplicates.jar I=SRR769316.bam O=SRR769316_duplicates_marked.bam M=SRR769316_duplicates.metrics.csv
-Note that in this command two output files are named, as the '''O=''' option (O for output) is for the new bam files with duplicates marked, and the '''M=''' (M for metrics) is for the output file contining metrics. Both filenames are of the user's choosing, though one expects the former will be a bam, and the latter a csv file.
+Note that in this command two output files are named, as the '''O=''' option (O for output) is for the new bam files with duplicates marked, and the '''M=''' (M for metrics) is for the output file containing metrics. Both filenames are of the user's choosing, though one expects the former will be a bam, and the latter a csv file.
 == Estimating gene count ==

← Older revision		Revision as of 21:21, 25 May 2016
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	== Quality Control of the mapping ==		== Quality Control of the mapping ==
		+
		+	Essentially this is made up of the MarkDuplicates step, though a read browser such as IGV should also be used to get familiarised with the data. The essential steps are:
		+
		+	To quickly see and a get a feel for alignment, use
		+	samtools view <bam_file> \|less -S
		+
		+	Then the MarkDuplicates step, using picard tools, which almost everybody uses for this:
		+
		+	java -jar $PICARD/MarkDuplicates.jar I=SRR769316.bam O=SRR769316_duplicates_marked.bam M=SRR769316_duplicates.metrics.csv
		+
		+	Note that in this command two output files are named, as the '''O=''' option (O for output) is for the new bam files with duplicates marked, and the '''M=''' (M for metrics) is for the output file contining metrics. Both filenames are of the user's choosing, though one expects the former will be a bam, and the latter a csv file.
		+

	== Estimating gene count ==		== Estimating gene count ==

@@ Line 1: / Line 1: @@
 = Introduction =
-This is based on Edinburgh Genomics' two day RNAseq course.
+This is based on Edinburgh Genomics' two day RNAseq course. The protocol it follows is started to get dated, as certain elements are now moving to updated methods. Neverthelesss it reflects more or less the standard set of procedures that have been used for the four years of 2012-2015.
-= Steps in Brief =
+= Steps =