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• clip adapter sequences
  Hello, I am trying to clip adapter sequences from fastq files, however when I open this tool it ...
• Clip Doesn'T See My Fastq File
  Hello, I'm using Galaxy on the PSU server. I uploaded a FASTQ file that I want t...
• PAR CLIP T to C change analysis
  Can you please tell me how can I look for T to C changes in my PAR CLIP data. It would be really ...
• Clip
  Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use th...
• Setting clipping sequence as workflow parameter when running FASTX Clipper from BioBlend API
  I am using the BioBlend API to run a workflow on Galaxy, and I am having trouble setting the para...
• Trimming
  Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy? and what ...
• How to remove soft clipping reads
  Hi Does anyone know a way or a tool to remove soft and hard clipping reads from the sam file usi...
• Illumina Clip Step in Trimmomatic
  In trimmomatic, under Perform Initial Illumina Clip step, which adapter sequence should I specify...
• 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...
• 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...
• Overlapping axis labels when graphing quality score box plot
  Hello~ Small SOS. I'm trying to graph the quality box plot and the nucleotide distribution chart...
• Primer Contamination, Miranalyzer
  Hi Galaxy, Ive got 2 problems for you; 1) Ive got microRNA Illumina NGS data that I want to ana...
• How To Clip Multiple Adapter Sequences In Penn State Galaxy? Thank.
  Hi All, In " Clip adapter sequences" option of Penn State Galaxy, I choose "Enter custom sequenc...
• 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...
• How To Clip Multiple Adapter Sequences In Penn State Galaxy? Thank.
  Hi All, In " Clip adapter sequences" option of Penn State Galaxy, I choose "Enter custom sequenc...
• 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...
• 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...
• Clip Adapter Sequence
  Good morning, I am very new in using Galaxy. I would like to use Clip to remove the adapter sequ...
• T to C mutations in PAR-CLIP
  HI: I am looking for a way to quantify T to C changes on my PAR-CLIP data. Tools such as Naive V...
• Analyzing Bowtie result
  Hi, I used bow tie tool in galaxy to align my reads from Miseq for small RNA sequences against h...
• Will not clip a fasta format file
  Hello, We used high throughput screening of small DNA fragments (about 100 base pairs long). The...