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• Number of aligned reads in exon, intron ...
  Hello,   I am new in RNA-seq. I would like to know how calculate the number (%) of aligned read...
• Reads detected/"spill over" on introns after using bamCoverage function from deepTools
  Hello! We recently used the recent version of bamCoverage from the deepTools suite for our ribo-s...
• Count intron retention reads from BAM files
  Hi there, How to find/filter intron-retained reads from BAM files? Which flag in BAM file descri...
• Filtering a Tophat BAM file
  Dear All, I have a  BAM file after Tophat2. When I checked it on Artemis after gene prediction u...
• Re-merge split BAM files
  Hi all, Let's say I have SAM/BAM files containing single-end reads. My reads look like: Intron 1...
• Calculate Percent Spliced In (PSI)
  Dear all, I was wondering if there is any tool to calculate PSI from the BAM files. Basically wh...
• Intersectbed/Coveragebed -Split Purify Exon?
  all.reads.bam file records mapped RNA-seq reads data, including: exon:exon junction exon body ...
• How do I get the read counts for a specific exon
  I have a bam file and a gtf file that contains a single line.... chr5 UCSC exon 1...
• Hg19 regions for Intergenic, Promoters, Enhancer, Exon, Intron, 5-UTR, 3-UTR and so on
  Hi guys,  I want to count the number for each feature: enhancer, promoter, exon, intron and so o...
• htseq counts on genes (introns + exons)
  Hello, I was wondering if there was a way of using htseq to count the number of reads per genes...
• How to count number of unique exons/introns (and their locations) in a GTF file?
  I have a large GTF file, I want the following information? * Number of unique exons * Number of ...
• Introduce OpenGene: an open source library for processing NGS data
  [OpenGene, core libraries for NGS data analysis and bioinformatics, written in julia][1] OpenGen...
• Count exon-exon junction reads for transcripts
  Dear all, I downloaded some bam files from TCGA, and I am hoping to count the exon-exon junction...
• Extracting Intron-Exon Reads from bam files
  I would like to extract intron-exon reads (unspliced reads) from bam file. I tried use the with ...
• FeatureCounts count reads per gene (Including Introns)
  Hi Everyone, I am using `featureCounts` to count the number of reads mapping to genes. ...
• Assembly of transcripts from junction reads
  I have a series of files containing exon-exon junctions, essentially chr, start, end, strand of e...
• Extract only RNA-seq reads in a BAM file that extend into an intron
  I have a BAM file containing many amplicon RNA-seq reads mapped to a small genomic region. Most ...
• is this a typo in this article?
  Hi. I was reading an article with title "topology entropy of DNA sequences". So, in the abstract,...
• How to classify chIP-seq reads into gene bins?
  Hello everyone! I am very new to RNA-seq data analysis. Your help on how to accomplish the below...