Changes between Version 9 and Version 10 of SOPs/rna-seq-diff-expressions_TE

Timestamp:

02/25/21 10:26:26 (3 years ago)

Author:

twhitfie

Comment:

--

SOPs/rna-seq-diff-expressions_TE

@@ -18 +18 @@
   * **Quantification of raw counts**
     * TEtranscripts uses the BAM file(s) of aligned reads (from STAR in this example) as input.
-    * TEtranscripts relies on separate gene annotation files (GTFs) for genes and TEs.  A curated collection of TE GTFs can be found [https://www.dropbox.com/sh/1ppg2e0fbc64bqw/AACUXf-TA1rnBIjvykMH2Lcia?dl=0 here].
+    * TEtranscripts relies on separate gene annotation files (GTFs) for genes and TEs.  A curated collection of TE GTFs can be found [https://www.dropbox.com/sh/1ppg2e0fbc64bqw/AACUXf-TA1rnBIjvykMH2Lcia?dl=0 here] and in the genome resources on the cluster at the Whitehead Institute (for human, mouse and fly).
     * Before assigning reads, it is important to know whether they are stranded (see the '''Quantification of raw counts''' section of our [http://barcwiki.wi.mit.edu/wiki/SOPs/rna-seq-diff-expressions best practices] page for details on how to determine this).
     * The best way to use the resources on the cluster to assign reads to genes and TEs is by running TEcount separately on each experiment (reverse stranded reads are shown in the example below, for forward stranded reads use --stranded forward and for unstranded reads use --stranded no (the default)):