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• What to do with Cuffquant .cxb files
  I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a ref...
• htseq-count no read align
  Hi I am trying to get raw count of mapped read, so I am running htseq-count on tophat accepted h...
• Normalization of RNA-seq data
  Hi, I am wanting to normalize my RNA-seq data without running a differential gene expression on...
• How do I get ribosomal RNA counts from featureCounts of my bam files?
  Hi, I used HISAT2 to align more RNAseq fastq files and then featureCounts to count my features. ...
• Galaxy app to retrieve selected raw reads
  There are many previous threads regarding how to retrieve selected raw reads from fastq files off...
• Raw Count Of Genes
  Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-inf...
• Duplicate row names error with EdgeR on FeatureCounts files
  Hi all, I created tabular count files using FeatureCounts with a GTF file (iGenomes, UCSC hg38) ...
• Uploading Gz Files
  I am unable to load the raw alignment data from the broad institute datasets available from the u...
• error using HTseq-count for conversion of .bam to raw counts
  Hello, I am trying to convert the .bam files I got as output from tophat alignment into raw coun...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...
• Workflow only runs first step and then stops
  Hello, I am trying to learn how to process RNA-Seq datasets with Galaxy to compute read counts pe...
• Extract reads from BAM file
  Hi I have a BAM file with all the reads aligned to the reference sequence that I used to map them...
• How To Get Reads Counts From Cufflins?
  Hi all, I got the normalized values (FPKM) from cufflinks. And I want to get relative reads co...
• DEXseq count reads tool obtaining only zero counts for all exons
  I'd like to run DEXseq on my RNA-seq dataset to identify any potential differences in exon inclus...
• Extracting Raw Count Data From Mapping
  Hi, I would like to extract raw counts from tophat output. Does anyone know a way to do this in...
• Count intervals of non-uniquely mapped reads overlapping the genome
  Hello everyone, I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm...
• RNA-Seq raw count data analysis using GALAXY
  Hi, I have downloaded the raw_readcounts files (.txt files) from an RNA-Seq experiment using GSE ...
• How to get rid of the linker of the miRNA raw data?
  How to get rid of the linker of the miRNA raw data? I want to use the raw data, but I don’t  know...
• Regarding reads extract from bam file
  Hello, Can anyone tell me that how can i get information of aligned reads using reads name from ...
• DiffBind on Galaxy
  Hi, I am trying to perform Diff Bind on Galaxy using output from MACS and bam files for Read and...
• Read counts for limited genome regions
  Hello: I would like to get raw reads depth at each genome position for a limited region of the c...
• 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...