1730ff9edd3add19e65f8b50f4d51052e3285cb1
brianlee
  Fri Feb 5 12:13:53 2021 -0800
Adding input from user on backslash on sed command and other fix and wget command to bigChain.html refs #26935

diff --git src/hg/htdocs/goldenPath/help/bigChain.html src/hg/htdocs/goldenPath/help/bigChain.html
index 00ca533..33483c3 100755
--- src/hg/htdocs/goldenPath/help/bigChain.html
+++ src/hg/htdocs/goldenPath/help/bigChain.html
@@ -73,39 +73,45 @@
 Download the <code>bedToBigBed</code> and <code>hgLoadChain</code> programs from the UCSC
 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p>
 <p>
 <strong>Step 4.</strong> 
 Use the <code>fetchChromSizes</code> script from the 
 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">same directory</a> to create a 
 <em>chrom.sizes</em> file for the UCSC database with which you are working (e.g., hg38). 
 Alternatively, you can download the 
 <em>chrom.sizes</em> file for any assembly hosted at UCSC from our 
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</a> page (click on &quot;Full 
 data set&quot; for any assembly). For example, the <em>hg38.chrom.sizes</em> file for the hg38 
 database is located at 
 <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" 
 target="_blank">http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>.</p>
 <p>
+Here are wget commands to obtain these above files.
+<pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/bigChain.as
+wget https://genome.ucsc.edu/goldenPath/help/examples/bigLink.as
+wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
+wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain
+</code></pre></p>
 <strong>Step 5.</strong> 
 Use the <code>hgLoadChain</code> utility to generate the <em>chain.tab</em> and <em>link.tab</em> 
 files needed to create the bigChain file:</p> 
-<pre><code>hgLoadChain -noBin -test hg38 bigChain chr22_KI2707731v1_random.hg38.mm10.rbest.chain</code></pre>
+<pre><code>hgLoadChain -noBin -test hg38 bigChain chr22_KI270731v1_random.hg38.mm10.rbest.chain</code></pre>
 <p>
 <strong>Step 6.</strong> 
 Create the bigChain file from your input chain file using a combination of <code>sed</code>, 
 <code>awk</code> and the <code>bedToBigBed</code> utility: 
-<pre><code>sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' &gt; chr22_KI270731v1_random.hg38.mm10.rbest.bigChain
+<pre><code>sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' &gt; chr22_KI270731v1_random.hg38.mm10.rbest.bigChain
 bedToBigBed -type=bed6+6 -as=bigChain.as -tab chr22_KI270731v1_random.hg38.mm10.rbest.bigChain hg38.chrom.sizes bigChain.bb</code></pre></p> 
 <p>
 <strong>Step 7.</strong> 
 To display your date in the Genome Browser, you must also create a binary indexed link file to 
 accompany your bigChain file:</p> 
 <pre><code>awk 'BEGIN {OFS="\t"} {print $1, $2, $3, $5, $4}' link.tab | sort -k1,1 -k2,2n &gt; bigChain.bigLink
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab bigChain.bigLink hg38.chrom.sizes bigChain.link.bb </code></pre>
 <p>
 <strong>Step 8.</strong> 
 Move the newly created bigChain (<em>bigChain.bb</em>) and bigLink (<em>bigChain.link.bb</em>)
 files to a web-accessible http, https or ftp location.</p>
 <p>
 <strong>Step 9.</strong> 
 Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single 
 <a href="hgTracksHelp.html#TRACK">track line</a>. Note that any of the track attributes listed