Eland - Revision history

Sgupta at 03:06, 12 November 2009

2009-11-12T03:06:18Z

Sgupta at 15:16, 6 October 2009

2009-10-06T15:16:29Z

Sgupta at 15:15, 6 October 2009

2009-10-06T15:15:58Z

Sgupta at 15:06, 6 October 2009

2009-10-06T15:06:21Z

Sgupta at 15:27, 10 September 2009

2009-09-10T15:27:38Z

Sgupta at 21:41, 9 September 2009

2009-09-09T21:41:00Z

Sgupta at 22:20, 1 September 2009

2009-09-01T22:20:52Z

Sgupta at 22:15, 1 September 2009

2009-09-01T22:15:01Z

New page

ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads with size up to 32 bp (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.

== To run the program ==

Step 1: Please copy the script titled - "run_eland.pl" - from "\\Gobo\wicmt_public\public_apps\ELAND" folder to your home directory.

Step 2: Copy the *_sequence.txt files from the "quality score" folders to your working directory where you have write permissions.

Step 3: Open the "run_eland.pl" in any text editor and modify the parameter according to the instructions in the file. Please email Sumeet Gupta, sgupta@wi.mit.edu, if you have any questions.

Step 4: Logon to your tak account.

Step 5: Run the perl script "run_eland.pl".

== Output Files ==

1. *_eland_extended.txt - Gives all the positions a read maps, if it matches to less than 10 positions.

2. *_export.txt - Contains all read, quality value and alignment information for a lane of data.

3. *.ylf - (Y)oung (L)ab (F)ormat files - These are used as input for the young lab error model for ChIP-Seq analysis.

4. *_sorted.txt - Contains all the uniquely mapped reads, sorted based on the position on the genome.

5. *_genomesize.xml - Summary for the genome being used for the alignment

6. TechnicalAnalysis-(*).xls - QC Report for the ELAND alignment - Please refer here for details - http://jura.wi.mit.edu/genomecorewiki/index.php/QCOutputFormat

← Older revision		Revision as of 03:06, 12 November 2009
Line 1:		Line 1:
−	ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads ~~with size up to 32 bp~~ (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.	+	ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for solexa reads (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.

	[[ELANDV1.1\|Version 1.1]]		[[ELANDV1.1\|Version 1.1]]

@@ Line 3: / Line 3: @@
 [[ELANDV1.1|Version 1.1]]
-Changes:
+Changes: <br>
-. Does not require the user to copy fastq input files from the source directory like solexa_public.
+. Does not require the user to copy fastq input files from the source directory like solexa_public.<br>
 . Does not require the user to copy the wrapper script to another directory. You can call it from the original destination by giving a full path to where the script lives.
-. Requires a config file which outlines all the parameters like input file, input directory, output directory, seed length etc.
+. Does not require the user to copy the wrapper script to another directory. You can call it from the original destination by giving a full path to where the script lives.<br>
 . User can submit multiple alignments to the cluster with different parameters.
 [[ELANDV1|Version 1.0]]
 Allows users to run the alignments for the whole genome using ELAND. The program uses the seed length to find all the possible matches for a particular read and then extends the seed upto the read length, scoring each position based on the quality scores, and picks the best possible alignment. In addition, it generates QC reports and other formats as soon as the alignment is finished.

← Older revision		Revision as of 15:15, 6 October 2009
Line 1:		Line 1:
	ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads with size up to 32 bp (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.		ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads with size up to 32 bp (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.
		+
		+	[[ELANDV1.1\|Version 1.1]]
		+
		+	Changes:
		+	1. Does not require the user to copy fastq input files from the source directory like solexa_public.
		+	2. Does not require the user to copy the wrapper script to another directory. You can call it from the original destination by giving a full path to where the script lives.
		+	3. Requires a config file which outlines all the parameters like input file, input directory, output directory, seed length etc.
		+	4. User can submit multiple alignments to the cluster with different parameters.
		+
		+	[[ELANDV1\|Version 1.0]]
		+
		+	Allows users to run the alignments for the whole genome using ELAND. The program uses the seed length to find all the possible matches for a particular read and then extends the seed upto the read length, scoring each position based on the quality scores, and picks the best possible alignment. In addition, it generates QC reports and other formats as soon as the alignment is finished.

← Older revision		Revision as of 15:06, 6 October 2009
Line 1:		Line 1:
	ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads with size up to 32 bp (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.		ELAND - E fficient L arge-Scale A lignment of N ucleotide D atabases - is an alignment tool integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads with size up to 32 bp (Cox, unpublished). Although the core program is a binary executable but we have built certain wrapper scripts to be able to run the ELAND program independently of the pipeline.
−
−	~~== To run the program ==~~
−
−	~~Step 1: Please copy the script titled - "run_eland_v1.pl" - from "\\Gobo\wicmt_public\public_apps\ELAND" folder to your home directory.~~
−
−	~~Step 2: Copy the *_sequence.txt files from the "quality score" folders to your working directory where you have write permissions.~~
−
−	~~Step 3: Open the "run_eland_v1.pl" in any text editor and modify the parameter according to the instructions in the file. Please email Sumeet Gupta, sgupta@wi.mit.edu, if you have any questions.~~
−
−	~~Step 4: Logon to your tak account.~~
−
−	~~Step 5: Run the perl script "run_eland_v1.pl".~~
−
−	~~== Output Files ==~~
−
−	~~1. [Prefix]_[GenomeUsed]_[SeedUsed]_eland_extended.txt - Gives all the positions a read maps, if it matches to less than 10 positions.~~
−
−	~~2. [Prefix]_[GenomeUsed]_[SeedUsed]_export.txt - Contains all read, quality value and alignment information for a lane of data.~~
−
−	~~3. [Prefix]_[GenomeUsed]_[SeedUsed].ylf - (Y)oung (L)ab (F)ormat files - These are used as input for the young lab error model for ChIP-Seq analysis.~~
−
−	~~4. [Prefix]_[GenomeUsed]_[SeedUsed]_sorted.txt - Contains all the uniquely mapped reads, sorted based on the position on the genome.~~
−
−	~~5. [Prefix]_[GenomeUsed]_[SeedUsed]_genomesize.xml - Summary for the genome being used for the alignment~~
−
−	~~6. TechnicalAnalysis-[Prefix]_[GenomeUsed]_[SeedUsed].xls - QC Report for the ELAND alignment - Please refer here for details - http://jura.wi.mit.edu/genomecorewiki/index.php/QCOutputFormat~~
−
−	~~7. [Prefix]_[GenomeUsed]_[SeedUsed]_tagcount.txt - Gives a count for all the reads, their corresponding counts, position on the genome and the gene name if it is in the transcribed region.~~

@@ Line 15: / Line 15: @@
 == Output Files ==
-. *[GenomeUsed]_[SeedUsed]_eland_extended.txt - Gives all the positions a read maps, if it matches to less than 10 positions.
+. [Prefix]_[GenomeUsed]_[SeedUsed]_eland_extended.txt - Gives all the positions a read maps, if it matches to less than 10 positions.
-. *[GenomeUsed]_[SeedUsed]_export.txt - Contains all read, quality value and alignment information for a lane of data.
+. [Prefix]_[GenomeUsed]_[SeedUsed]_export.txt - Contains all read, quality value and alignment information for a lane of data.
-. *[GenomeUsed]_[SeedUsed].ylf - (Y)oung (L)ab (F)ormat files - These are used as input for the young lab error model for ChIP-Seq analysis.
+. [Prefix]_[GenomeUsed]_[SeedUsed].ylf - (Y)oung (L)ab (F)ormat files - These are used as input for the young lab error model for ChIP-Seq analysis.
-. *[GenomeUsed]_[SeedUsed]_sorted.txt - Contains all the uniquely mapped reads, sorted based on the position on the genome.
+. [Prefix]_[GenomeUsed]_[SeedUsed]_sorted.txt - Contains all the uniquely mapped reads, sorted based on the position on the genome.
-. *[GenomeUsed]_[SeedUsed]_genomesize.xml - Summary for the genome being used for the alignment
+. [Prefix]_[GenomeUsed]_[SeedUsed]_genomesize.xml - Summary for the genome being used for the alignment
 . TechnicalAnalysis-[Prefix]_[GenomeUsed]_[SeedUsed].xls - QC Report for the ELAND alignment - Please refer here for details - http://jura.wi.mit.edu/genomecorewiki/index.php/QCOutputFormat
-. *[GenomeUsed]_[SeedUsed]_tagcount.txt - Gives a count for all the reads, their corresponding counts, position on the genome and the gene name if it is in the transcribed region.
+. [Prefix]_[GenomeUsed]_[SeedUsed]_tagcount.txt - Gives a count for all the reads, their corresponding counts, position on the genome and the gene name if it is in the transcribed region.

@@ Line 3: / Line 3: @@
 == To run the program ==
-Step 1: Please copy the script titled - "run_eland.pl" - from "\\Gobo\wicmt_public\public_apps\ELAND" folder to your home directory.
+Step 1: Please copy the script titled - "run_eland_v1.pl" - from "\\Gobo\wicmt_public\public_apps\ELAND" folder to your home directory.
 Step 2: Copy the *_sequence.txt files from the "quality score" folders to your working directory where you have write permissions.
-Step 3: Open the "run_eland.pl" in any text editor and modify the parameter according to the instructions in the file. Please email Sumeet Gupta, sgupta@wi.mit.edu, if you have any questions.
+Step 3: Open the "run_eland_v1.pl" in any text editor and modify the parameter according to the instructions in the file. Please email Sumeet Gupta, sgupta@wi.mit.edu, if you have any questions.
 Step 4: Logon to your tak account.
-Step 5: Run the perl script "run_eland.pl".
+Step 5: Run the perl script "run_eland_v1.pl".
 == Output Files ==