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comparison htseq-count.xml @ 11:f320093f1e8e

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Removed sorting notice from help
author lparsons
date Mon, 10 Dec 2012 13:36:54 -0500
parents 5d969cb56112
children 62a1de8c8aae
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10:5d969cb56112 11:f320093f1e8e
176 each gene is considered here as the union of all its exons. One may also consider 176 each gene is considered here as the union of all its exons. One may also consider
177 each exon as a feature, e.g., in order to check for alternative splicing. For 177 each exon as a feature, e.g., in order to check for alternative splicing. For
178 comparative ChIP-Seq, the features might be binding regions from a pre-determined 178 comparative ChIP-Seq, the features might be binding regions from a pre-determined
179 list. 179 list.
180 180
181 **Paired-end Data MUST be sorted by QUERY NAME first**
182
183 This tool requires that paired-end data be sorted by query name, which is NOT the default for Galaxy. Using the Picard Paired Read Mate Fixer with Query name sort FIRST is required for paired end data.
184
185 181
186 Overlap Modes 182 Overlap Modes
187 ------------- 183 -------------
188 184
189 Special care must be taken to decide how to deal with reads that overlap more than one feature. 185 Special care must be taken to decide how to deal with reads that overlap more than one feature.
193 The following figure illustrates the effect of these three modes: 189 The following figure illustrates the effect of these three modes:
194 190
195 .. image:: /static/images/count_modes.png 191 .. image:: /static/images/count_modes.png
196 :width: 500 192 :width: 500
197 193
194
198 Strandedness 195 Strandedness
199 ------------ 196 ------------
200 197
201 **Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data! 198 **Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!
199
202 200
203 Output 201 Output
204 ------ 202 ------
205 203
206 The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely 204 The script outputs a table with counts for each feature, followed by the special counters, which count reads that were not counted for any feature for various reasons, namely