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, 18:41, 23 November 2014
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| ** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line | | ** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line |
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− | [[File:gcalignStart.png|850px]] | + | [[File:gcalignStartNew.png|850px]] |
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| This should take 1-3 minutes to run. | | This should take 1-3 minutes to run. |
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− | It should end with a line like: <code>Processing finished in 133 secs with no errors reported</code> | + | It should end with a line like: <code>Processing finished in 47 secs with no errors reported</code> |
| + | * The <code>WARNING</code> messages are just to let you know that the default Read Group field settings are being used. |
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| If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off. | | If you cancelled GotCloud part way through, just rerun your GotCloud command and it will pick up where it left off. |
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| Inside GotCloud align, not only sequence alignment but also pre-processing of sequence data, including deduplication and base quality recalibration are performed along with quality assessment, as illustrated below. | | Inside GotCloud align, not only sequence alignment but also pre-processing of sequence data, including deduplication and base quality recalibration are performed along with quality assessment, as illustrated below. |