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More tweaking to try to get Cuffdiff to pass functional tests. The problem is that Cuffdiff's output is not deterministic, so lines_diff needs to be large enough (but no larger than needed) to accomodate small differences in output.

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Jeremy Goecks
2010-10-27 17:59:07 -04:00
parent 8ebd691f06
commit acbc070a66
1 changed files with 1 additions and 1 deletions
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tools/ngs_rna/cuffdiff_wrapper.xml
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@@ -77,7 +77,7 @@
Line diffs are needed because cuffdiff does not produce deterministic output.
TODO: can we find datasets that lead to deterministic behavior?
-->
<output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/>
<output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/>
<output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/>
<output name="tss_groups_exp" file="cuffdiff_out3.txt"/>
<output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>