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• find mean, standard deviation, max, and min for insert lengths in BWA
  Hello how can I find mean, standard deviation, max, and min for insert lengths in BWA?
• Cuffdiff Changes
  Hi, I am wondering why Cuffdiff suddenly gives many more significant DE genes? I have used same ...
• How to set 'mean inner distance' for paired-end reads?
  Hi all, If I use Paired-end sequences for 'Tophat for illumina' or 'Tophat 2', I need to type in...
• Insert sizes in Galaxy
  I am new to RNASeq analysis. I used tophat to generate BAM files from FASTQ files but in the para...
• Cuffdiff Errors: "Loading reference annotation" and "Inspecting maps and determining fragment length distributions". whats that mean?
  Hello everybody, I'm very new in RNA seq analysis I have run cuffdiff on 3 condition dataset coll...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• Are reads number normalized on transcript length ?
  Hello, I used featurecounts to obtain reads number from a RNA-seq file (.bam). I would know if t...
• BWA-MEM Fatal error: Matched on ERROR
  Hi, I was aligning with bwa-mem on a 52.7GB trimmed paired fastq from WGS under the following con...
• CuffDiff error on Local Galaxy
  HI, I am running local instance of Galaxy on my linux mint system. When I try to run CuffDiff, ...
• Error while running cuffdiff "Fatal error: Exit Code 1()"
  Hello, I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18...
• Read length from HT-Seq
  Hi, Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial ada...
• Reconstruct original fragment from paired end reads
  Hi, I would like to reconstruct my environemental 16S PCR fragments (slightly more than 300 bp) ...
• Cuffdiff error- Fatal error: Exit code 139 ()
  Hi, I am getting the following error while running Galaxy cuff diff. An error occured with t...
• Assembling PE reads with broad fragment length distribution
  Hi, I am sequencing some very degraded DNA with 2X75bp PE. I have retained very short fragments ...
• Tophat can run negative r
  Regarding to Mean Inner Distance between Mate Pairs, I tried run ~1000000 reads twice: (1) if r...
• Read Length Distribution
  Hi, Is there a tool or easy way to obtain a read length distribution on a set of 454 reads in fa...
• Tophat "Mean Inner Distance Between Mate Pairs"
  Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distanc...
• Cuffdiff 2.2.1.5 error with cummeRbund SQlite. "Fatal error: Exit code 1 () -- use version 2.2.1.3 instead
  Hi, so as a disclaimer, I am very new to RNA seq analysis. I received the following error while r...
• How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA
  Hi everyone, Having mapped the reads (paired-end) to a reference genome using BWA, I am trying t...