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• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Comparing the Single and Paired End Assemblies
  Hello there!   Im using this touorial to analyze and assembly mate pair NGS reads for my illumi...
• Paired-end Reads trimming
  Hey there. I am starting to analyse some RNAseq paired-end data. At the pre-processing step I go...
• Merging Of Illumina Paired End Files
  I have 3 illumina paired end reads of exome capture of the sample. I want to assemble these reads...
• Making paired-end reads the same length
  I have paired-end data (in two separate files).  I have groomed my files, and would like to filte...
• Assembly Of Paired And Unpaired Sequences
  Dear All Greetings! I am analysing a genome of ca. 3.4Mb where I have paired.fa and unpaired.fa ...
• miSEQ data analysis
  I have the miSeq paired end reads as two different fastaq files. How can I assemble/merge them th...
• Troubles in de novo assembly of an insect genome
  I need to assemble an insect genome. The genome size is around 500Mb. I have performed genome seq...
• Question About Using Bowtie
  I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I have data from paired en...
• Considerations for trimming poor quality Illumina MiSeq paired end reads
  I have generated fastq files from Illumina MiSeq for bacterial genome sequencing. My reads are 2...
• Trinity with multiple datasets
  Hello, I am running trinity on 4 data sets (2 left reads, 2 right reads) and I want it to be com...
• How Much Can I Trimm My Reads
  Dear All, I am analysing RNA-seq datasets for the differential splicing events between cell type...
• Galaxy-using trimmomatics with ChIP seq pair ended (only one file with both reads)
  I am trying to run Trimmomatics in Galaxy under "pair end (as collection)" for afastqsanger.gz ...
• 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...
• Preprocessing of mate paired end read sequences for de novo genome assembly
  I have just started out in the field of genome assembly, so please bear with my lack of knowledge...
• 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...
• Bacterial Sequence for Variant Analysis
  I am analyzing paired-end data for bacterial genome and have done the following steps: *FAST...
• Do I trim paired end sets first or merge and then trim?
  Hi there, I have a quick question - I have raw 10Gb -sized datasets for my samples. For each one...
• How can I do trimming off to all nucleotide sequences that end with a specific sequence in my illumine reads?!
  Hello everyone, I am new to Galaxy and I was wondering if anybody knows how can I trim all seque...
• Can Galaxy Help With Comparative Genomics?
  The lab I work with would like to compare a few populations' genomes of a species with an unpubli...