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comparison cuffnorm_wrapper.xml @ 5:9a854107dbb2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
author iuc
date Fri, 03 Jul 2020 11:44:40 -0400
parents 6cbfede05833
children 28b94cfbfdb9
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4:6cbfede05833 5:9a854107dbb2
1 <tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.2"> 1 <tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.3">
2 <description>Create normalized expression levels</description> 2 <description>Create normalized expression levels</description>
3 <macros> 3 <macros>
4 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
208 208
209 ------ 209 ------
210 210
211 **Input format** 211 **Input format**
212 212
213 Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples. 213 Cuffnorm takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
214 214
215 ------ 215 ------
216 216
217 **Outputs** 217 **Outputs**
218 218
221 Cuffnorm will report both FPKM values and normalized, estimates for the number of fragments that originate from each gene, transcript, TSS group, and CDS group. Note that because these counts are already normalized to account for differences in library size, they should not be used with downstream differential expression tools that require raw counts as input. 221 Cuffnorm will report both FPKM values and normalized, estimates for the number of fragments that originate from each gene, transcript, TSS group, and CDS group. Note that because these counts are already normalized to account for differences in library size, they should not be used with downstream differential expression tools that require raw counts as input.
222 To see the details of the simple table format used by Cuffnorm, refer to the simple table expression format, simple table sample attribute format, and simple table feature (e.g. gene) attribute format sections below. 222 To see the details of the simple table format used by Cuffnorm, refer to the simple table expression format, simple table sample attribute format, and simple table feature (e.g. gene) attribute format sections below.
223 223
224 ------- 224 -------
225 225
226 **Settings** 226 **Parameter list**
227 227
228 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. 228 This is a list of implemented Cuffnorm options::
229
230 ------
231
232 **Cuffdiff parameter list**
233
234 This is a list of implemented Cuffdiff options::
235 229
236 --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile 230 --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile
237 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags 231 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
238 --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. 232 --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
239 --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator 233 --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator