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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 07674fe3507909d11d7431e3b8c48afcfb1f4b5e"
author rnateam
date Tue, 07 Jun 2022 09:22:45 +0000
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bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
rnateam
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1 Important notes
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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2 ----------------
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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4 - At least 2 cores should be used for running ``ribotaper part 3: ribosome profiling``, therefore please configure **job_conf.xml** accordingly.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
rnateam
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6 - We ran the RiboTaper analysis on an SGE cluster, using 7 cores and h_vmem 8G. For each dataset, the complete RiboTaper workflow (from the bam files to final results) took ~ 1 day.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
rnateam
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bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
rnateam
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8 - The current RiboTaper framework is not designed to identify and quantify ORFs on different transcripts. This means the transcript annotation is crucial.
bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
rnateam
parents:
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bade631353d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 9a59864f0bfb9937309d2c18b8cf3715c8067808
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10 - Be careful about using scaffolds, both in the genome and GTF files, which may slow the whole pipeline.