deea5ecd50c17260a1d3e43ed7c36af0401241d7 gperez2 Sat Dec 31 14:58:42 2022 -0800 Fixing 404 link for the Static Page Cronjob 2022-12-15, no RM diff --git src/hg/htdocs/goldenPath/help/blatSpec.html src/hg/htdocs/goldenPath/help/blatSpec.html index 4c48c8e..0d27dee 100755 --- src/hg/htdocs/goldenPath/help/blatSpec.html +++ src/hg/htdocs/goldenPath/help/blatSpec.html @@ -47,31 +47,31 @@ <p> Other programs in the blat suite are: <ul> <li> <a href="#pslSortUsage">pslSort</a> – combines and sorts the output of multiple blat runs. The blat default output format is <a href="../../FAQ/FAQformat.html#format2">psl</a>.</li> <li> <a href="#pslRepsUsage">pslReps</a> – selects the best alignments for a particular query sequence, using a "near best in genome" approach.</li> <li> <a href="#pslPrettyUsage">pslPretty</a> – converts alignments from psl format, which is a tab-delimited format that does not include the bases themselves, to a more readable alignment format.</li> <li> <a href="#faToTwoBitUsage">faToTwoBit</a> – converts - <a href="http://genetics.bwh.harvard.edu/pph/FASTA.html" target="_blank">fasta</a> format sequence + <a href="https://arep.med.harvard.edu/seqanal/fasta.html" target="_blank">fasta</a> format sequence files to the dense, randomly accessible <a href="../../FAQ/FAQformat.html#format7">.2bit</a> format that gfClient can use.</li> <li> <a href="#twoBitToFaUsage">twoBitToFa</a> – converts from .2bit format back to fasta format.</li> <li> <a href="#faToNibUsage">faToNib</a> – converts from fasta to the somewhat less dense, randomly accessible <a href="../../FAQ/FAQformat.html#format8">.nib</a> format that predated .2bit format. Note that each .nib file can contain only a single sequence.</li> <li> <a href="#nibFragUsage">nibFrag</a> – converts portions of a .nib file back to fasta format.</li> </ul> <p> Usage details for each of the above programs are described in the sections below. For all programs