== [http://jura.wi.mit.edu/bio BaRC] Standard operating procedures ==

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.
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=== Short read sequencing ===

* [wiki:SOPs/qc_shortReads Quality control and preprocessing of short reads (fastq files)][[br]] [[br]]
* [wiki:SOPs/mapping Mapping short reads ][[br]] [[br]]
* [wiki:SOPs/miningSAMBAM SAM/BAM summarizing and processing][[br]] [[br]]
* [wiki:SOPs/SAMBAMqc SAM/BAM quality control][[br]] [[br]]
* [wiki:SOPs/chip_seq_peaks Using ChIP-Seq to identify and/or quantify bound regions (peaks) ][[br]] [[br]]
* [wiki:SOPs/Using ngsplot to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq peaks) ][[br]] [[br]]
* [wiki:SOPs/Using ngsplot to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq peaks) ][[br]] [[br]]
* [wiki:SOPs/rna-seq-diff-expressions Using RNA-Seq to quantify gene levels and assay for differential expression][[br]][[br]]
* [wiki:SOPs/AssemblingRNAseqReads Using RNA-Seq to assemble or annotate transcripts ][[br]] [[br]]
* [wiki:SOPs/integrateExpressionIP Integrating expression and immunoprecipitation experiments][[br]] [[br]]
* [wiki:SOPs/geneFeatureHeatmaps Creating genome feature heatmaps from sequencing experiments][[br]] [[br]]
* [wiki:SOPs/gzipping Creating an analysis pipeline of compressed files][[br]] [[br]]

=== Variant calling and analysis ===

* [wiki:SOPs/variant_calling Using Samtools' mpileup/bcftools to call variants from short-read sequencing][[br]] [[br]]
* [wiki:SOPs/variant_calling_GATK Using GATK to call variants from short-read sequencing][[br]] [[br]]
* [wiki:SOP/CallingVariantsRNAseq Calling variants from RNA-seq data] [[br]] [[br]]
* [wiki:SOPs/vcf_manipulation Manipulating VCF files ][[br]] [[br]]
* [wiki:SOPs/vcf Interpreting VCF files ][[br]] [[br]]

=== Genome coordinates and genomics ===

* [wiki:SOPs/coordinates Creating genome coordinate files (bed, wig, etc) for genome browsers ][[br]] [[br]]
* [wiki:SOPs/genome_regions_annotations Linking genome regions to genome annotation(s)  ][[br]] [[br]]
* [wiki:SOPs/subsequences Extracting genome subsequences ][[br]] [[br]]
* [wiki:SOPs/homologous Identifying homologous genes/proteins ][[br]] [[br]]

=== Microarrays ===

* [wiki:SOPs/normalize_ma Normalizing and preprocessing microarrays][[br]] [[br]]
* [wiki:SOPs/diff_microarry Identifying differentially expressed genes from microarrays][[br]] [[br]]
* [wiki:SOPs/normalizePublic Normalizing multiple public microarray datasets][[br]] [[br]]

=== Enrichment analysis ===

* [wiki:SOPs/enriched_tf_binding_sites Identifying all and/or enriched transcription factor binding sites ][[br]] [[br]]
* [wiki:SOPs/go_annotation Identifying enriched GO or other annotation terms in a set of genes ][[br]] [[br]]

=== Statistics ===

* [wiki:SOPs/StatisticalSteps Performing and reporting statistical tests][[br]] [[br]]
* [wiki:SOPs/calculating_variation Calculating variation (SD, SE) for a ratio ][[br]] [[br]]
* [wiki:SOPs/anova Performing ANOVA in R][[br]] [[br]]

=== Other topics ===

* [wiki:SOPs/multipleSequenceAlignment Producing a multiple sequence alignment of proteins, transcripts, or genome regions][[br]] [[br]]
* [wiki:SOP/PatternsMotifs Searching for patterns or motifs in a DNA or protein sequence] [[br]] [[br]]
* [wiki:SOPs/clusteringMatrixHeatmap Clustering a matrix and creating a heatmap][[br]] [[br]]
* [wiki:SOPs/chipSeqBakeoffResults ChIP-Seq analysis bake-off results][[br]] [[br]]

=== [wiki:SOPs/InProgress In Progress] ===
* [wiki:SOPs/ShortReadExpDesign Experimental design of short read sequencing experiments][[br]] [[br]]
* [wiki:SOP/MassSpec Mass spectrometry data analysis] [[br]] [[br]]