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66 bytes added
, 21:14, 18 March 2015
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| ====Outputs==== | | ====Outputs==== |
− | Upon successful completion of the *recab* sub-pipeline, you should see the following files/subdirectories under the user specified output directory: | + | Upon successful completion of the *recabQC* sub-pipeline, you should see the following files/subdirectories under the user specified output directory: |
| *'''recab/mergedBams/''' - contains merge results | | *'''recab/mergedBams/''' - contains merge results |
| ** '''''*/SAMPLE.merged.bam'' - a merged BAM file''' | | ** '''''*/SAMPLE.merged.bam'' - a merged BAM file''' |
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| *** '''''*/SAMPLE.qplot.stats'' - sample statistics''' | | *** '''''*/SAMPLE.qplot.stats'' - sample statistics''' |
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− | You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *recab* sub-pipeline failed. | + | You should see .done and .OK files for each SAMPLE in the index file. If you do not see the .done and .OK files, then your *recabQC* sub-pipeline failed. |
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− | '''On success, the recab/ folder contains the final BAMs and bais.''' | + | '''On success, the recab/ folder contains the final BAMs and bais, while the QCFiles/ folder contains the quality control output''' |
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| ===Command-Line and Configuration Options=== | | ===Command-Line and Configuration Options=== |