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• Error with "Trim leading or trailing characters" tool
  Hi all, I have been trying to trim my fastq files, and I am running into problems. I used the "T...
• >90% aligned concordantly 0 times ChIP-seq Bowtie2
  Hi, I know this question have raised many times here and in other forums but I've tried everythi...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Error due to format of uploaded fastq data
  Hello Everyone, I am a new to RNA-Seq and Galaxy. I tried to analyse my RNA-Seq data from RAT (...
• 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...
• Pre-Processing Of Illumina Rna-Seq Paired End Data
  Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically ...
• Cuffdiff Error after cuffmerge or cuffcompare
  Hi everyone, I'm doing a transcriptome of zebrafish, 2 replicates for each condition of 3 conditi...
• 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...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• GEO SRA fastq-dump with very low mapping rate (Galaxy)
  Dear Biostars, I am a quite unexperienced biologist doing a metaanalysis of RNA-seq/microarray e...
• Mark Duplicates - MAPQ = 0 and Value was put into PairInfoMap more than once
  Dear Biostars Galaxy team, I'm relatively new to using the Galaxy online platform and have been ...
• SAMtools Merge BAM files hangs
  Hi all, I am using TopHat to map RNA-seq reads. My study species is a non-model organism, so I c...
• SAM to BAM conversion
  I have seen that I am not the first one to have the problem: the SAM to BAM conversion (either di...
• Primer Contamination, Miranalyzer
  Hi Galaxy, Ive got 2 problems for you; 1) Ive got microRNA Illumina NGS data that I want to ana...
• Any tools for separate unpaired reads in paired-end sequencing fastq files?
  Hi, I would like to know if there is any tool can do the following job? I have some data files ...
• Fastq To Fastqsanger Using Groomer Question
  Hello! I am fairly new to using Galaxy and have a question about the FASTQ Groom...
• Filter synthax for nested conditionals
  Hello, I write a tool and I have a problem with the outputs generated : My script is : <to...
• Fastq Joiner Problem
  Hi, I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq j...
• What is the correct regular expression for replacing inconsistent sequence and quality identifiers?
  Hello, I am trying to analyze RNA-Sequence data. The SRA accession number for the file that I am...
• adding some tools into galaxy using xml
  HEY guys, I have got some problems.I want to add a tool into galaxy.But following the xml below,w...
• Storing Compressed Data Files
  Hello, As users add more and more data files to our galaxy server, disk space becomes a problem....