3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Sequence Mapping and Assembly Practical, December 2014 (view source)
Revision as of 18:41, 23 November 2014
, 18:41, 23 November 2014→Run GotCloud Align
** 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
[[File:gcalignStart.png|850px]]
[[File:gcalignStartNew.png|850px]]
This should take 1-3 minutes to run.
This should take 1-3 minutes to run.
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.
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.
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.
