b44df11903f0c8537dc9d716df324906bc89f92b lrnassar Thu Jun 15 13:21:32 2023 -0700 Adding documentation supporting snakes rearrangement display, refs #31241 diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html index 0ea7326..e97207e 100755 --- src/hg/htdocs/FAQ/FAQformat.html +++ src/hg/htdocs/FAQ/FAQformat.html @@ -270,31 +270,33 @@ chr11 5246919 5246920 Hb_North_York 2619 Hemoglobin variant chr11 5255660 5255661 HBD c.1 G>A 2659 delta0 thalassemia chr11 5247945 5247946 Hb Sheffield 2672 Hemoglobin variant chr11 5255415 5255416 Hb A2-Lyon 2676 Hemoglobin variant chr11 5248234 5248235 Hb Aix-les-Bains 2677 Hemoglobin variant

To see an example of turning a bedDetail custom track into the bigBed format, see this How to make a bigBed file blog post.

PSL format

PSL lines represent alignments, and are typically taken from files generated by BLAT or psLayout. See the BLAT -documentation for more details. All of the following fields are required on each data line +documentation for more details. PSL data tracks can also be visualized in +rearrangement +display mode. All of the following fields are required on each data line within a PSL file:

  1. matches - Number of bases that match that aren't repeats
  2. misMatches - Number of bases that don't match
  3. repMatches - Number of bases that match but are part of repeats
  4. nCount - Number of "N" bases
  5. qNumInsert - Number of inserts in query
  6. qBaseInsert - Number of bases inserted in query