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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 6ede79703d2f4ed200c5e1d273cad674be486900"
author rnateam
date Wed, 08 Jun 2022 15:05:03 +0000
parents a56343c142d5
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a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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1 Important notes
a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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2 ----------------
a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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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.
a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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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.
a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
rnateam
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a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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.
a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
rnateam
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a56343c142d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 8e6fdb45c70ba778280df5b222036f3b5c604cdf
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10 - Be careful about using scaffolds, both in the genome and GTF files, which may slow the whole pipeline.