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• What to do when alignment rate is low even though the genomic data and RNA-seq data are of same stain
  Hello While doing RNA-seq analysis, when I mapped reads for each condition to the reference gen...
• Tophat2 align_summary interpretation
  Hello, I'm examining my tophat output data and I would like to have some opinions on my align_su...
• TopHat align summary
  Hello, I am using galaxy to analyze RNA seq of 100bp sing end data, sequenced with Illumina 2500...
• the meaning of tophat alignment summary
  hi,there is a question about tophat alignment summary,would you please answer for me ,thank you v...
• TopHat Align Summary - whats a good results
  Howdy, Just got the results back from top hap - looked at align summary Not sure how to read it...
• 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 ...
• analysis of tophat results
  hi i have done qc and then groomed single end sra sequences from ebi. i ran tophat. i am getting...
• tophat result interpretation
  i have downloaded an SRA sequence from ebi. after doing QC and grooming i have run tophat. i have...
• Low mapping of paired-end reads with tophat2
  Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage...
• TOPHAT MAPPED READS
  Hi, i am using the RNA seq pipeline for transcriptome analysis. i ahve the annotation anf gff fi...
• Can Tophat Take Snps Into Account?
  Hi, I have been mapping my RNA-seq data to mouse genome from a different mouse strain using TopHa...
• 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...
• 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...
• Bowtie alignment with multiple datasets
  Dear community, I am now in the process of aligning RNA-seq reads with Bowtie2. My input is a li...
• About Mapping Quality
  Hi all, I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the value of s...
• Mapping With Tophat Vs. Bwa
  Hello, I am getting what seems to me to be strange results using two different mapping tools in ...
• miRNA sequencing alignment
  i have a rna-seq data and would like to align it against micro RNA human. Can I do it in galaxy. ...
• Alignment rate differes using hg19 and hg38
  I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the bui...