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• 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...
• HISAT2 soft clipping
  When using default options HISAT2 performs soft clipping. Under scoring options soft clipping is...
• Illumina Clip Step in Trimmomatic
  In trimmomatic, under Perform Initial Illumina Clip step, which adapter sequence should I specify...
• Removing a single base from 3' end of the reads using "Clip" option
  Hello, I need to remove a single base i.e. C from the 3' end of all of my reads. I tried doing i...
• Galaxy showing and hiding tools as refreshed?
      I have installed some tools, but when I click on Galaxy logo and on Analyse data I see tool...
• Clipping adapter from 3' end of only 1 of 2 paired end reads
  Hi all, I cropped barcodes a long while back in a lab where I had CLC Genomics - now that I'm in...
• Are all the starting BED coordinates generated by BWA matching the first base of the reads ?
  I am currently using "Map with BWA for illumina" (in galaxy main server) with default settings to...
• Primer Contamination, Miranalyzer
  Hi Galaxy, Ive got 2 problems for you; 1) Ive got microRNA Illumina NGS data that I want to ana...
• How do i remove multiple adapter sequences from my RNAseq reads?
  Hi there, I want to remove the universal adapters as well as the index adapters in each data fil...
• Clip
  Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use th...
• Output of FLASH can't be read by other tools?
  Hi, I have used FLASH to assemble some reads. They are still in FASTq format. However I can't ge...
• Fastq-Mcf
  Hi all, Does someone know fastq-MCF? We are relatively newbies in analysing RNAseq results, and w...
• 3' Adapter Trimming Using Fastx-Toolkit Clipper
  Hi all, I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5 M reads. I wan...
• Remove "Unpaired" Reads From Quality-Filtered Pared-End Fastq Files.
  Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality usi...
• 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...
• Trimming Illumina Reads From 3' Without Considering Quality Score
  Is it possible to trim certain number of bases from 3' end with taking into consideration quality...
• Remove e. coli and vector contaminants from Ilumina reads
  I ran Trinity (wheat 300 bp paired ends) using Ilumina reads. When I ran BLAST on the contigs, so...
• removing of duplication in RNA seq
  Hi I am new in bioinformatics and in Galaxy too so please bear with me Soon I will have RNA seq...
• Trinity analysis error before to start ?normalization? fastdump?
  Good morning everyone My trinity analysis is stucked before to start. I wonder what is the hipot...