Changes between Version 6 and Version 7 of SOPs/rna-seq-diff-expressions_TE

Timestamp:

02/24/21 20:41:33 (4 years ago)

Author:

twhitfie

Comment:

--

SOPs/rna-seq-diff-expressions_TE

@@ -10 +10 @@
     * Use [https://github.com/alexdobin/STAR STAR] or another spliced mapper to map short reads to the genome of choice.
     * See our [http://barcwiki.wi.mit.edu/wiki/SOPs/mapping mapping SOP] to search for details on running STAR.
-    * When assessing transcription of TEs, it is ''essential'' to include multi-mapping reads.  When using STAR, in particular, the winAnchorMultimapNmax and outFilterMultimapNmax flags are used to control multimapping, the former by setting a lower bound on how many loci must have a matching seed and the latter defining the upper bound on how many loci a read maps to in order to report it.  A command for STAR mapping paired end reads using gzipped fastq input can look like:
+    * When assessing transcription of TEs, it is ''essential'' to include multi-mapping reads.  When using STAR, in particular, the winAnchorMultimapNmax and outFilterMultimapNmax flags are used to control multimapping, with the former setting a lower bound on how many loci must have a matching seed and the latter defining the upper bound on how many loci a read maps to in order to report it.  A command for STAR mapping paired end reads using gzipped fastq input can look like:
 
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