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• 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...
• Way to trim all NGS nucleotide sequences to a specific section
  Is there a way to trim the nucleotide sequence to a specific region? I know you can by base numbe...
• 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...
• How Much Can I Trimm My Reads
  Dear All, I am analysing RNA-seq datasets for the differential splicing events between cell type...
• Help removing part of a sequence
  Hi, I am trying to trim out part of a sequence so I can align it better to a reference sequence....
• Re: Quality Based Trimming
  Thanks for your reply Daniel. That's right... I did not even think about using the boxplot tool t...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• Pe Reads D Ont Map After Trimming
  Hi, I hoped that someone could shed some light onto this . I am attempting to map a set of 2x 1...
• Trimming sequences with homology parameters
  Hello, I am processing single-end illumina reads coming from a PCR library.  I know the flankin...
• 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...
• 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...
• Shortening Sequences?
  Hi All, I have a little how to do question and was hoping somebody knows the answer? I have a me...
• Question About Using Bowtie
  I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I have data from paired en...
• 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...
• Trimmomatic Operation Error
  Hi, I try to trim my sequence with trimmomatic. But I cannot understand why my options are not ta...
• Problem running Clustal 2.1 Multiple Sequences Alignment - an instance of 'std::bad_alloc'
  Dear All, I've been trying to analyze reads from a short transcript. The data I have was obtaine...
• 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...
• genome de novo assembly
  Hello, I have a paired-end 150 bp genome sequencing data with a different end quality.According ...
• Download Bowtie2 alignment
  Hi, I have done a saturation mutagenesis experiment and sequenced the resulting PCR products via...
• trimmomatic with paired-end
  Dear Biostar, I have paired-end sequencing data I would like to trim using trimmomatic. I have r...
• 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 ...
• how to find adaptor sequences
  Hi    How can i find the adaptor sequence in my reads.
• 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...