CoReFinder - Revision history

Philippbayer: /* Prerequisites */

2016-04-07T04:10:59Z

‎Prerequisites

Philippbayer: /* Convert .soap to sorted .bam */

2016-03-08T03:05:24Z

‎Convert .soap to sorted .bam

Philippbayer: /* Prerequisites */

2016-03-08T03:00:51Z

‎Prerequisites

Philippbayer: /* Custom script for coverage analysis - CoReFinder */

2016-03-08T03:00:17Z

‎Custom script for coverage analysis - CoReFinder

Philippbayer at 02:47, 8 March 2016

2016-03-08T02:47:35Z

Philippbayer at 02:47, 8 March 2016

2016-03-08T02:47:20Z

Philippbayer: /* Questions */

2016-03-08T02:47:00Z

‎Questions

Philippbayer: /* Prerequisites */

2016-03-08T02:46:39Z

‎Prerequisites

Philippbayer at 02:46, 8 March 2016

2016-03-08T02:46:20Z

Philippbayer: /* Mapping */

2016-03-08T02:43:18Z

‎Mapping

@@ Line 35: / Line 35: @@
 . R
-. CoRefinder from Bhavna Hurgobin [http://appliedbioinformatics.com.au/download/compareCoverage_V7_BH.R download]
+. CoRefinder from Bhavna Hurgobin [http://appliedbioinformatics.com.au/download/compareCoverage_V9_BH.R download]
 ==Mapping==

@@ Line 49: / Line 49: @@
 ==Convert .soap to sorted .bam==
-Use SOAP's soap2sam.pl and samtools view -bS to convert to bam, and sort using samtools sort, then index bam file (samtools index)
+Use SOAP's soap2sam.pl:
 ==Finding per base coverage using Bedtools==

← Older revision		Revision as of 03:00, 8 March 2016
Line 34:		Line 34:

	4. R		4. R
		+
		+	5. CoRefinder from Bhavna Hurgobin [http://appliedbioinformatics.com.au/download/compareCoverage_V7_BH.R download]

	==Mapping==		==Mapping==

@@ Line 68: / Line 68: @@
 ==Custom script for coverage analysis - CoReFinder ==
-[path DOWNLOAD]
+[http://appliedbioinformatics.com.au/download/compareCoverage_V7_BH.R DOWNLOAD]
 R script to categorise regions of interest based on various statistics:

@@ Line 106: / Line 106: @@
-=== FAQ ===
+= FAQ =
 To come
-=== Questions ===
+= Questions =
 Please feel free to ask Philipp at philipp.bayer@uwa.edu.au if anything comes up!

← Older revision		Revision as of 02:47, 8 March 2016
Line 111:		Line 111:

	== Questions ==		== Questions ==
		+
		+	Please feel free to ask Philipp at philipp.bayer@uwa.edu.au if anything comes up!

@@ Line 27: / Line 27: @@
 ==Prerequisites==
-. bedtools from http://soap.genomics.org.cn/soapaligner.html - at least version v2.25.0, so that genomecov -d reports positions with 0 reads aligning
+. bedtools from https://github.com/arq5x/bedtools2 - at least version v2.25.0, so that genomecov -d reports positions with 0 reads aligning
 . SOAPaligner from http://soap.genomics.org.cn/soapaligner.html

@@ Line 1: / Line 1: @@
-CoReFinder
+CoReFinder - a pipeline to find collapsed and repetitive regions in genome assemblies
 =Methodology=
@@ Line 13: / Line 13: @@
 ==Repeated/non-collapsed region==
 If we map reads to the reference with –r0, there will be regions where reads do not map. This could happen because of a number of reasons: the region is not in the raw data, the region in the genome where we want to map the reads contain N's or tiny repetitive regions or more likely that they represent large duplicated regions in the assembly. Because the reads can map to more than one place, using -r0 will discard them. If we map the same reads to Darmor with –r1, and identify regions empty with –r0 but covered with –r1 then these are duplicated in the assembly. Also, if we map reads with -r2, a duplicated, non-collapsed region should have roughly half of the reads in -r1 compared to -r2, a triplicated region should have roughly a third etc.
 ==Repetitive/collapsed region==
 Coverage higher than the average coverage with -r0, -r1 and -r2 will be repetitive/collapsed regions of the assembly. This is because these reads have nowhere else to map in the genome, so they will pile up at the collapsed portion of the assembly.
 ==Zero or low coverage regions==
 Zero or very low coverage with -r0, -r1 and -r2.
 =Pipeline=
 ==Mapping==
 Align reads to the reference genome (indexed using 2bwt-builder) using each of -r0, -r1 and -r2:
@@ Line 90: / Line 104: @@
 The above regions could be merged into a single region (9101920 to 9103794), and in this way when we are looking for genes in this entire region, we are less likely to miss them compared to if we were looking at smaller regions.

@@ Line 25: / Line 25: @@
 Align reads to the reference genome (indexed using 2bwt-builder) using each of -r0, -r1 and -r2:
-   soap -p4 -r0 -v 2 -m 0 -x 1000 -a /scratch/y82/bhurgobin/Brassica/DarmorV8/raw_reads/10x/Darmor_10x_R1_aa.fastq -b /scratch/y82/bhurgobin/Brassica/DarmorV8/raw_reads/10x/Darmor_10x_R2_aa.fastq -o /scratch/y82/bhurgobin/Brassica/DarmorV8/raw_reads/10x/Darmor_10x_R1_aa.fastq.paired.soap -2 /scratch/y82/bhurgobin/Brassica/DarmorV8/raw_reads/10x/Darmor_10x_R1_aa.fastq.single.soap -u /scratch/y82/bhurgobin/Brassica/DarmorV8/raw_reads/10x/Darmor_10x_R1_aa.fastq.unmapped.soap
+   soap -p 4 -r 0 -v 2 -m 0 -x 1000 -a R1_library.fastq -b R2_library.fastq -o Output.paired.soap -2 Output.single.soap -u Output.unmapped.soap
 Three types of outputs are produced from the SOAP mappings: paired mapped reads, single/unpaired mapped reads, unmapped reads. We only use the paired mapped reads for the coverage analysis.