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 "Full data set" 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}' > 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}' > 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 > 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