Changes between Version 1 and Version 2 of blastTips

Timestamp:

12/01/22 10:50:03 (18 months ago)

Author:

gbell

Comment:

--

blastTips

@@ -127 +127 @@
   * Note that databases indexed for old-style blastall (using formatdb) work fine with blast+.
 
-=== Filtering BLAST results===
-  * Limiting or filtering hits: do not use max_target_seqs.  Based on [[https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 | Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows]], this parameter does not return the top/best hit(s)!  Instead, get all hits and filter downstream as needed.
+=== Using more restrictive BLAST options ===
 
+Limiting or filtering hits can be done by the following options, which are all a bit different:
+
+  * -max_target_seqs => Maximum number of aligned sequences to keep (value of 5 or more is recommended; incompatible with num_descriptions, num_alignments)
+  * -num_descriptions => Number of database sequences to show one-line descriptions for
+  * -num_alignments => Number of database sequences to show alignments for
+
+Requiring higher-confident hits than the defaults can also be useful
+
+  * -evalue => Expectation value (E) threshold for saving hits (default = 10); can be reduced to 0.1 or even 1e-10 (depending on the reason for doing the BLAST search)
+
+