4d62fae590223b48c28c0212f3422176cd80e2f7 brianlee Wed Feb 17 10:22:44 2021 -0800 Adding a note about the input referenceDb that came up in bigMaf MLQ refs #27009 diff --git src/hg/htdocs/goldenPath/help/bigMaf.html src/hg/htdocs/goldenPath/help/bigMaf.html index c084221..f4c3bd0 100755 --- src/hg/htdocs/goldenPath/help/bigMaf.html +++ src/hg/htdocs/goldenPath/help/bigMaf.html @@ -82,30 +82,33 @@ <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">directory</a>.</p> <p> <strong>Step 5.</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> <pre><code>mafToBigMaf hg38 chr22_KI270731v1_random.maf stdout | sort -k1,1 -k2,2n > bigMaf.txt bedToBigBed -type=bed3+1 -as=bigMaf.as -tab bigMaf.txt hg38.chrom.sizes bigMaf.bb </code></pre> +<p>Note that the hg38 in the mafToBigMaf hg38 command indicates the referenceDb and matches the +expected prefix of the primary species' sequence name, for instance hg38 for the +hg38.chr22_KI270731v1_random found in the input example chr22_KI270731v1_random.maf file.</p> <p> <strong>Step 6.</strong> Follow the below steps to create the binary indexed mafFrames and mafSummary files to accompany your bigMaf file:</p> <pre><code>genePredSingleCover chr22_KI270731v1_random.gp single.gp genePredToMafFrames hg38 chr22_KI270731v1_random.maf bigMafFrames.txt hg38 single.gp bedToBigBed -type=bed3+8 -as=mafFrames.as -tab bigMafFrames.txt hg38.chrom.sizes bigMafFrames.bb hgLoadMafSummary -minSeqSize=1 -test hg38 bigMafSummary chr22_KI270731v1_random.maf cut -f2- bigMafSummary.tab | sort -k1,1 -k2,2n > bigMafSummary.bed bedToBigBed -type=bed3+4 -as=mafSummary.as -tab bigMafSummary.bed hg38.chrom.sizes bigMafSummary.bb </code></pre> <p> <strong>Step 7.</strong> Move the newly created bigMaf file (<em>bigMaf.bb</em>) to a web-accessible http, https or ftp location. If you generated the <em>bigMafSummary.bb</em> and/or <em>bigMafFrames.bb</em> files,