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• Counting reads supporting a specific splice junction from bam file
  Hi, How can I count the number of reads supporting a specific splice junction (e.g. chr1:15000-2...
• Splice prediction from bam files
  Are there any command line tools that specialize in predicting splice site variants from bams?
• Filtering out the spliced reads from bam file.
  Hi, I have bam file and I would like to filter out spliced reads from the bam file. How can I ac...
• Alternative splicing analysis
  Is there an alternative splicing tool that will take in my bam alignment and produce alternative ...
• Cufflinks error: BAM record error: found spliced alignment without XS attribute
  I got RNA-seq bam files that are aligned by BWA. When I am using these bam files in cuflinks I go...
• To determine the number of correct splice junctions from the alignment output from HISAT2
  Hi, I am new to Bioinformatics and programming but can follow a clear program in order to arriv...
• Given a bam file, obtain read numbers that traverse a specific exon junction
  Hello group, I have a list of exons from several genes that are differentially spliced between...
• Interpreting splice junctions on IGV
  I am currently analyzing some RNA-seq data. I am using STAR for my alignment and am looking for a...
• Can Cufflinks Handle Bam Files From Outside?
  By bam from outside, I mean the alignment made not by TopHat. Here in Using Cufflinks for RNA-Se...
• spliced alignment algorithm
  The picture is a view of an rna-seq bam file from tophat alignment. On the left side, in red, ar...
• Cuffdiff Error on Galaxy
  hello I am trying to run cuffdiff on use galaxy server but I keep on running into the same error:...
• How to count novel and known splice junction reads from BAM
  Hi, I have BAM file from TopHat 2 alignment with RefSeq genes annotation. Is there any way to co...
• Splitting the Spliced reads from genome Alignment
  Hi, I have a RNA-seq reads mapped onto genome using tophat2 and obtained a "bam" file which is l...
• hisat2-cufflinks: BAM record error: found spliced alignment without XS attribute
  I got alignment by using hisat2 with reference genome, and sort the sam file to bam file. when I ...
• Splicing in virus using long read sequencing
  Hello, I am working on a project where long read sequencing was done using PacBio for a virus ge...
• Using Cufflinks For Rna-Seq Without Tophat/Bowtie.
  Hi, I was wondering if anyone has successfully used Cufflinks in combination with an aligner fr...
• Determing number of spliced alignments in a BAM file
  What is the best way of determining the number of spiced alignments in a BAM file with SAMTOOLS? ...
• splicing with UMI barcodes - paired end illumina sequencing
  Hello, I have 250 bps paired end illumina sequencing reads with UMIs. I am interested in identif...
• Splice junction sites and number of splitted reads from STAR aligned bam
  Hi everyone! I'm working with some RNA-seq bams aligned with STAR. What I want to do is to detec...
• How To Extract the total number of Spliced junctions from several biological replicates
  Hi All I have 6 RNA-Seq datasets (biological replicates). How can extract the total number of sp...