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Pipeline publication

[…] e.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegTfbsClustered/and used for the overlap studies , . All Italian, Singapore-Chinese and 1000 Genome Project's rare and prevalent variants were tested for overlap with the TFBSs and compared to randomly selected UCE positions (G/C content corrected). Random UCE sets contained equal number of positions to the rare or prevalent variants in the corresponding data sets., For the Super-Enhancer SNVs overlap, one hundred sets of 1000 random rare or prevalent SNVs were selected and each set was tested for TFBSs overlap. From this the mean overlap and 95% confidence intervals was calculated. Random positions selection and all overlap studies were done by BEDTools shuffleBed and intersectBed tools, respectively ., 1000 Genome phase1 version3 variants were downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ ., Super-enhancer regions were obtained from the study by Whyte et.al . Mouse to human conversion was done by the liftOver tool (http://genome.ucsc.edu/cgi-bin/hgLiftOver)., RNA secondary structure predictions were made by RNAsnp perl script which allows large-scale analysis . RNSsnp Mode 1 was used with default parameters, except minimum length of the sequence interval was set to 25. Parameter descriptions can be found from the RNAsnp Web Server (http://rth.dk/resources/rnasnp/)., All statistical calculations and figures were produced using R and its packages., We analyzed single nucleotide variations (SNVs) within 2884 UCE regions that span ∼1.39 Mb of the human genome (). In order to resequence this relatively large set of elements in a comprehensive and economical manner we used a pooled sample targeted sequencing strategy, a cost effective and reliable approach for population resequencing studies , . We had access to samples from two different ancestries: 501 samples from an Italian population (ITA) and 280 samples from a Singaporean Chinese cohort (SG-CHN) (). All samples were pooled by population and gender w […]

Pipeline specifications

Software tools BEDTools, liftoveR, RNAsnp Web Server
Organisms Homo sapiens