Difference between revisions of "Eland"
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== Output Files == | == Output Files == | ||
| − | 1. | + | 1. [Prefix]_[GenomeUsed]_[SeedUsed]_eland_extended.txt - Gives all the positions a read maps, if it matches to less than 10 positions. |
| − | 2. | + | 2. [Prefix]_[GenomeUsed]_[SeedUsed]_export.txt - Contains all read, quality value and alignment information for a lane of data. |
| − | 3. | + | 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. | + | 4. [Prefix]_[GenomeUsed]_[SeedUsed]_sorted.txt - Contains all the uniquely mapped reads, sorted based on the position on the genome. |
| − | 5. | + | 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 | 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. | + | 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. |
Revision as of 11:27, 10 September 2009
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integrated in Illumina-Solexa data processing package, can do ungapped alignment for reads with size up to 32 bp (Cox, unpublished).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.
