== [http://barc.wi.mit.edu/ BaRC] Best practices ==

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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Frequently Asked Questions (of particular interest to Whitehead scientists) are on our [http://barcwiki.wi.mit.edu/wiki/FAQ FAQs site].
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=== General short-read sequencing ===

* [wiki:SOPs/qc_SRA Downloading and processing NCBI SRA files][[br]] [[br]]
* [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/geneFeatureHeatmaps Creating genome feature heatmaps from sequencing experiments][[br]] [[br]]
* [wiki:SOPs/gzipping Creating an analysis pipeline of compressed files][[br]] [[br]]
* [wiki:SOPs/ShortReadExpDesign Experimental design of short read sequencing experiments][[br]] [[br]]
=== Specific types of short-read sequencing experiments ===

* [wiki:SOPs/rna-seq-diff-expressions Using RNA-Seq to quantify gene levels and assay for differential expression][[br]][[br]]
* [wiki:SOPs/rna-seq-diff-expressions_TE Using RNA-Seq to quantify gene levels and assay for differential expression including transposable elements][[br]][[br]]
* [wiki:SOPs/AssemblingRNAseqReads Using RNA-Seq to assemble or annotate transcripts ][[br]] [[br]]
* [wiki:SOPs/chip_seq_peaks Using ChIP-Seq to identify and/or quantify bound regions (peaks) ][[br]] [[br]]
* [wiki:SOPs/atac_Seq Using ATAC-Seq to identify open chromatin ][[br]] [[br]]
* [wiki:SOPs/Hi-C Using Hi-C experiments to characterize genome-wide chromatin structure ][[br]] [[br]]
* [wiki:SOPs/HiChIP Using HiChIP experiments to characterize genome-wide chromatin contacts between regulatory elements ][[br]] [[br]]
* [wiki:SOPs/RRBS Using RRBS experiments to characterize genomic DNA methylation  ][[br]] [[br]]
* [wiki:SOPs/integrateExpressionIP Integrating expression and immunoprecipitation experiments][[br]] [[br]]
* [wiki:SOPs/CUT&Tag Using CUT&Tag to identify DNA bound regions and chromatin marks][[br]] [[br]]

=== Single-cell genomics ===

* [wiki:SOP/scRNA-seq Single cell RNA-seq analysis] [[br]] [[br]]
* [wiki:SOP/Demultiplex_HTO_ADT_data Demultiplexing scRNA-seq hashtag oligos (HTOs)] [[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]]

=== Structural biology ===

* [wiki:SOPs/AlphaFold Predicting protein structures from sequence using AlphaFold][[br]] [[br]]
* [wiki:SOPs/AlphaFoldMultimer Predicting the structures of protein complexes using AlphaFold multimer][[br]] [[br]]

=== Other topics ===

* [wiki:SOPs/Using Using ngsplot to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq peaks) ][[br]] [[br]]
* [wiki:SOPs/multipleSequenceAlignment Producing a multiple sequence alignment of proteins, transcripts, or genome regions][[br]] [[br]]
* [wiki:SOP/MassSpec Mass spectrometry data analysis] [[br]] [[br]]
* [wiki:SOP/NanoString NanoString data analysis] [[br]] [[br]]
* [wiki:SOP/PooledCRISPR Pooled CRISPR screen analysis] [[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/submittingSequencingToGEO Submitting a sequencing dataset to GEO][[br]] [[br]]