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• Job failures at http://usegalaxy.org 2016-12-12
  dear galaxy team i am working on human single end illumina data i want to imprve the mapping alig...
• 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...
• Analyzing Targeted Resequencing Data With Galaxy
  Hi! I am having problems with my sequencing results, but I am a newbie at this; so I am thinking ...
• Analysing paired end RNAseq data with poor quality score
  Hello, I'm new in NGS and i'm currently working on RNA-seq. I had 6G of illumina reads and proce...
• Bowtie
  Hi Experts, I have single end Illumina reads from ChIP-Seq experiment. The files have encoding I...
• 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 ...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• 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...
• Preprocessing Gdna Illumina Paired End Data For Mapping/Snp Calling
  This question is w/ regards to pre-processing whole genome resequencing data for mapping data to ...
• What is the difference between the tools "BWA" and and "Map with BWA for illumina" - tolerated mismatches at sequence end
  Hi, What is the difference between the tools "BWA" and and "Map with BWA for illumina"  ? I rea...
• 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 ...
• BWA for Illumina
  Hello, I'm starting to use Galaxy, and I'm trying to generate vcf and BAM files from my Fastq (pa...
• Asking About Allignment Figure
  Hello, I am sorry, I did not know about the appropriate address ( galaxy-user@bx.psu.edu) for as...
• How to know if mapping to reference genome was succesful?
  Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overvi...
• Paired end illumina RNAseq reads - running trinity with paired trimmed files and adding unpaired as single read?
  We have paired end Illumina HiSeq 4000 reads that we are working to remove adaptors and trim base...
• BWA error [bwa_aln] 17bp reads: max_diff = 2
  I wish to align single end fastq sample using "Map with BWA" tool. The reads were trimmed several...
• What format of data required for Mapping with Bowtie
      I am a new user of Galaxy. Recently, got some next gen RNAseq data from Illumina single end...
• Filter Fastq By Percentage Of Ambiguous (N) Bases
  Hello, I like to filter my fastq files (50 bp single end Illumina RNA seq reads) by a maximum th...
• Macs
  while using MSCS tool from Galaxy I get following mesg. with BED file: "Treatment tags and Contr...
• NGS mapping via Bowtie on paired end trimmed files is failing
  Hi Galaxy support, I have ran paired end files for a staphylococcus aureus genome (Illumina Mis...
• Help! I'm using trimmomatic in Galaxy, but it doesn't recognize a part of input dataset.
  I'm using Trimmomatic to trimming paired end reads. When I set "Single-end or paired-end reads?"...
• mapping NGS data with BWA for Illumina
  Hello!   i am trying to map single-end reads using BWA for Illumina but an error accoured: Er...
• Trimming sequences with homology parameters
  Hello, I am processing single-end illumina reads coming from a PCR library.  I know the flankin...