2a702699cb3b42282222e2bb9d0947cb03baac75 gperez2 Wed Sep 21 18:19:32 2022 -0700 Made a few minor edits to barChart.html_example7, refs #29984 diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index 46d1a23..0a88112 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -458,64 +458,64 @@ by numerical value or alphabetical name.</p> <p> Also, if you click the "Return to Genome Browser" link, you will see only these selection bars are displayed.</p> <div class="text-center"> <img src="../../images/barChartFacets4.png" alt="Example4 of Facets on barCharts" width="700"> </div> <p> In this image after making the selections browsing ACE2 the "zoom out" button has been clicked to also view nearby genes where the expression of these tissue selections for the gene PIR is quite noticeably different.</p> <h6 id="example7">Example #7</h6> <p> In this example, we will be using command-line tools that were used to create the single-cell tracks -available on hg38. For a more in-depth examples of these tools, take a look at the following +available on hg38. For more in-depth examples of these tools, take a look at the following <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/makeDb/doc/hg38/gtex.txt#L711" target="_blank">makedoc</a> for a real-life example. </p> <p> The <code>matrixClusterColumns</code> command converts a single cell gene expression matrix to a cell-type gene expression matrix. It takes a cell-by-cell metadata matrix that refers to the same cells as a gene expression matrix and combines the gene expression values for all cells of a given type into a single value representing the cell type. It can also be used on other metadata fields to produce matrices that show mean or average gene expression levels for a donor, an organ, or any -other metadta field or combination of fields. The following command uses the +other metadata field or combination of fields. The following command uses the <a href="/goldenPath/help/examples/barChart/singleCell/exprMatrix.tsv">exprMatrix.tsv</a> and <a href="/goldenPath/help/examples/barChart/singleCell/meta.tsv">meta.tsv</a> files to create six files: prepMatrix.tsv, prepStats.tsv, TissueCompMatrix.tsv, TissueCompStats.tsv, SexMatrix.tsv, and SexStats.tsv. </p> <pre> matrixClusterColumns exprMatrix.tsv meta.tsv \ prep prepMatrix.tsv prepStats.tsv \ "Tissue Composition" TissueCompMatrix.tsv TissueCompStats.tsv \ Sex SexMatrix.tsv SexStats.tsv Read 5 rows from meta.tsv matrix exprMatrix.tsv has 209126 fields 209126 total columns, 209121 unclustered, 0 misses 209126 total columns, 209121 unclustered, 0 misses 209126 total columns, 209121 unclustered, 0 misses . </pre> <p> If you are not sure which GENCODE Genes version is best suited for your data, the <code>gencodeVersionForGenes</code> command takes a list of gene symbols or gene accessions and searches for the version of GENCODE or RefSeq that matches the most genes in the list. Optionally, -the tool can produces a BED file containing the gene structures for the genes in the list. +the tool can produce a BED file containing the gene structures for the genes in the list. The following command uses the <a href="/goldenPath/help/examples/barChart/singleCell/gene.lst">gene.lst</a> and <a href="/goldenPath/help/examples/barChart/singleCell/geneSymVerTx.tsv">geneSymVerTx.tsv</a> files to create a mapping.bed file that will be used in the next step. </p> <pre> # Figure out gene set gencodeVersionForGenes -target=hg38 gene.lst geneSymVerTx.tsv -bed=mapping.bed examining 23 versions of gencode and refseq best is gencodeVM5 as sym on mm10 with 6 of 6 (100%) hits on hg38 6 of 6 (100%) hit across versions </pre> <p>