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• This job was terminated because it used more memory than it was allocated
  Hello, I have always encountered such problem "This job was terminated because it used more memo...
• Please Help Me Check The Quality Of The Tophat Mapping To Reference Genome
  Dear All, I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat output (the...
• Error using stringtie - AttributeError: 'NoneType' object has no attribute"
  Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr...
• How to filter FASTQ by QS & length using galaxy tools in the command line?
  Problem I am stuck on how to implement filtering on the command line using the galaxy tools. Spe...
• Bowtie on Galaxy - -v or -n ?
  Good morning, I'm using Galaxy with Bowtie for Illumina to map smallRNA sequencing (illumina) on ...
• Re: Quality Based Trimming
  Thanks for your reply Daniel. That's right... I did not even think about using the boxplot tool t...
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• 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 ...
• Filtering BAM files from HISAT2
  Hi. I am new to rna-seq and I have a couple of quick questions. My input was paired-end non-stran...
• Minimum Length Of Read Segments
  Dear All, I am going to run Tophat with RNA-seq dataset to observe alternative splicing events. ...
• using mPileup to examine allelic imbalance in hybrids
  Hi, I have some RNA-seq data for two different species and their hybrids. I want to look at the ...
• Length of reads in a RNAseq experiment
  Should all the reads of my experiment be of the same length if I am going to perform a de novo a...
• Need help with "FASTQ Trimmer" tool
  FASTQ Trimmer seems unable to recognize my FASTQ files as input. For e.g. I carried out FASTQ to ...
• Trimmomatic Input Values
  Hello- I am using Trimmomatic to improve the quality of my RNA-seq data. I am using the followi...
• Bowtie2/FreeBayes/mpileup variant detection on NGS of PCR amplicons around Cas9/CRISPR indels
  Hey threre, I have an MiSeq experiment using 24 indices where in each index I was sequencing 3 P...
• Trimmomatic Operation Error
  Hi, I try to trim my sequence with trimmomatic. But I cannot understand why my options are not ta...
• Pe Reads D Ont Map After Trimming
  Hi, I hoped that someone could shed some light onto this . I am attempting to map a set of 2x 1...