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• trimmomatic with paired-end
  Dear Biostar, I have paired-end sequencing data I would like to trim using trimmomatic. I have r...
• trimgalore on interleaved paired-end fastq files
  Hi, I'm analyzing interleaved paired-end fastq files downloaded via fastq-dump. I am trying to r...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• 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 ...
• 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...
• 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...
• How to prepare FastQ files for HISAT2
  Hi there, Should I be preparing or otherwise cleaning fastq files before I try to align them to ...
• bam to fasta
  Hello, I am very new to dealing with NGS data.  Have followed the instructions on how to get pai...
• 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...
• Paired-end insert size upper limit
  I am mapping paired-end reads using Bowtie2 and setting "maximum insert size for valid paired-end...
• Trimmomatic and Trim Galore are not working.
  I am performing an RNA-seq and am trying to trim adapter sequences with Trim Galore. When I made ...
• Trimmomatic and adapters
  Hi all, As relatively new within the bioinformatics world, I am a bit confused when it comes to ...
• Trim Galore version - Adapter sequence
  Hello, I have been using Galaxy's Trim galore for clipping adapters from Illumina small RNA sequ...
• Read length from HT-Seq
  Hi, Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial ada...
• How To Analyze Genes Differential Expression Using Galaxy? Thanks.
  Hi All, Now I have two  Paired-End samples data ( they are  Next Generation Sequence Data and fa...
• MNase ChIP-seq paired-end data analysis ?
  Hello everyone! Sorry for long explanation! I did paired-end ChIP-seq for my input and IP sample...
• 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...
• Convert multiple FASTQ files into one BAM file
  Hello guys! I recently started working with NGS analysis and I may have a stupid question to ask....
• Clip
  Hi, I was using the clip program, but my adapters are on the 5' end. Is there any way to use th...
• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• 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?"...