| | 1 | |
| | 2 | == BaRC Standard operating procedures == |
| | 3 | |
| | 4 | These are "how-to's" detailing the methods that BaRC uses and finds to work effectively. Email BaRC if you have any questions about how or why to perform what is described on these pages. |
| | 5 | [[br]] [[br]] |
| | 6 | |
| | 7 | === Short read sequencing === |
| | 8 | |
| | 9 | * [wiki:SOPs/qc_shortReads Quality control and preprocessing of short-read sequencing ][[br]] [[br]] |
| | 10 | * [wiki:SOPs/chip_seq_peaks Using ChIP-Seq to identify and/or quantify bound regions (peaks) ][[br]] [[br]] |
| | 11 | * [wiki:SOPs/rna-seq-diff-expressions Using RNA-Seq to quantify gene levels and assay for differential expression][[br]][[br]] |
| | 12 | * [wiki:SOPs/AssemblingRNAseqReads Using RNA-Seq to assemble or annotate transcripts ][[br]] [[br]] |
| | 13 | * [wiki:SOPs/integrateExpressionIP Integrating expression and immunoprecipitation experiments][[br]] [[br]] |
| | 14 | * [wiki:SOPs/miningSAMBAM Summarizing, mining, and processing SAM/BAM files][[br]] [[br]] |
| | 15 | * [wiki:SOPs/callingSNPs Calling SNPs from Short-Read Sequencing][[br]] [[br]] |
| | 16 | * [wiki:SOPs/geneFeatureHeatmaps Creating genome feature heatmaps from sequencing experiments][[br]] [[br]] |
| | 17 | |
| | 18 | === Genome coordinates and genomics === |
| | 19 | |
| | 20 | * [wiki:SOPs/coordinates Creating genome coordinate files (bed, wig, etc) for genome browsers ][[br]] [[br]] |
| | 21 | * [wiki:SOPs/genome_regions_annotations Linking genome regions to genome annotation(s) ][[br]] [[br]] |
| | 22 | * [wiki:SOPs/subsequences Extracting genome subsequences ][[br]] [[br]] |
| | 23 | * [wiki:SOPs/homologous Identifying homologous genes/proteins ][[br]] [[br]] |
| | 24 | |
| | 25 | === Microarrays === |
| | 26 | |
| | 27 | * [wiki:SOPs/normalize_ma Normalizing and preprocessing microarrays][[br]] [[br]] |
| | 28 | * [wiki:SOPs/diff_microarry Identifying differentially expressed genes from microarrays][[br]] [[br]] |
| | 29 | * [wiki:SOPs/normalizePublic Normalizing multiple public microarray datasets][[br]] [[br]] |
| | 30 | |
| | 31 | === Enrichment analysis === |
| | 32 | |
| | 33 | * [wiki:SOPs/enriched_tf_binding_sites Identifying all and/or enriched transcription factor binding sites ][[br]] [[br]] |
| | 34 | * [wiki:SOPs/go_annotation Identifying enriched GO or other annotation terms in a set of genes ][[br]] [[br]] |
| | 35 | |
| | 36 | === Statistics === |
| | 37 | |
| | 38 | * [wiki:SOPs/calculating_variation Calculating variation (SD, SE) for a ratio ][[br]] [[br]] |
| | 39 | * [wiki:SOPs/StatisticalStepes Performing and reporting statistical tests][[br]] [[br]] |
| | 40 | * [wiki:SOPs/anova Performing ANOVA in R][[br]] [[br]] |
| | 41 | |
| | 42 | === Other topics === |
| | 43 | |
| | 44 | * [wiki:SOPs/multipleSequenceAlignment Producing a multiple sequence alignment of proteins, transcripts, or genome regions][[br]] [[br]] |
| | 45 | * [wiki:SOPs/clusteringMatrixHeatmap Clustering a matrix and creating a heatmap][[br]] [[br]] |
| | 46 | * [wiki:SOPs/chipSeqBakeoffResults ChIP-Seq analysis bake-off results][[br]] [[br]] |
| | 47 | |
| | 48 | === [wiki:SOPs/InProgress In Progress] === |
