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• randomly shuffle BAM file
  Is there a tool like bedtools shuffle which I can use to randomly shuffle a bam file? or will I h...
• Ajdust for GC content bias in RNA-seq DE analysis.
  When I was reading this paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471...
• InsideDNA: How to use BEDTools for analysis of genome methylation
  BEDTools is an extensive suite of utilities for genomic features analysis. There are several comm...
• Random shuffling of features leaving gene models intact
  I am looking for a tool that can randomly shuffle gff features into intergenic regions, but leavi...
• Customising bedtools shuffle command
  Hi, I am trying to use the bedtools shuffle command to shuffle transcription factor binding locat...
• How to compute the AT/GC ratio for an e.coli sequence in a fasta file?
  Last week I started a course in computing for ecology/evolution and am very new to this. We've be...
• Genomic feature overlaps taking into account underlying sequence feature distributions
  Dear Biostars, Once again I am here consulting your knowledge. I have studied binding sites for ...
• Correcting odd GC bias in whole-exome CNV calling
  This image shows the log2 ratio of tumor coverage over control coverage for each exon capture reg...
• On Calculating I-Traq Ratio
  Here is an worked out example of calculation of Normalized intensity ratio for i-TRAQ reporter io...
• Calculation of CpG ratio within X nucleotides
  Hello again, i need to calculate the CpG ratio within certain DNA sequences in order to correlat...
• Generating genome regions with matched length and GC-content
  Hi! I'm trying to generate regions of mm9 with matched length and GC-content to my existing file....
• Detecting GC Bias in Transcriptomes (RNA-seq)
  What's the best way to detect GC bias in a transcriptome (RNA-seq)? We are currently aligning...
• Converting Bedgraph to coverage
  I downloaded a dataset from your the UCSC Genome Browser- "Table Browser" with the following inpu...
• Graphing GC Bias in Sequence Capture
  Anyone have recommendations for making a chart like this for sequence capture? Picard CollectGcB...
• Genomic Regions To Exclude Before Shuffling Intervals
  I want to do permutation test: randomly reposit (shuffle) given genomic intervals and measure int...