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• extract only unique mapped paired end reads
  Hello,  I aligned paired end reads with bwa 0.5.9. Next, I would like to extract only paired end...
• How to get only paired end or single end uniquely mapped reads with Bowtie2?
  Hello, I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a ref...
• Mapped paired-end reads with Bowtie2
  Hi Biostar community, I have paired-end reads for MeDIP-seq. I'm able to mapped read1 and read2 ...
• Question About Using Bowtie
  I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I have data from paired en...
• Mapping Paired End Reads With Tophat
  Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped read...
• Tophat Paired End Read
  Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping...
• Low mapping of paired-end reads with tophat2
  Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage...
• Why are the SOLiD mapping functions gone?
  I noticed that under the NGS mapping section, all of the SOLiD functions are gone. Are they only ...
• Cufflinks Returned 0 Value In All Rpkms
  Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me ...
• Help!! Tophat Paired End Reads
  Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. ...
• Aligning more than 2 sequences
  I have a pair-end data fast1.fq and fast2.fq in (fastq format). Now, I need to align the pair-end...
• combining indexed paired reads from two lanes of a Hiseq rapidrun
  Hi I am doing paired end RNAseq, I have a single multiplexed pool that was run over both lanes o...
• Structurefold Iterative Mapping Input Fastq
  Regarding the tool structurefold, iterative mapping on Galaxy accepts one fastq at a time as inpu...
• 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...
• Tophat Mapping
  Hi, After mapping RNA-Seq paired end reads with Tophat, I can see that most of reads fall into...
• Tophat "Mean Inner Distance Between Mate Pairs"
  Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distanc...
• How to check unaligned reads?
  I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against ...
• Splitting Biased Paired End FASTQ data
  The FASTQ splitter in Galaxy warns that the tool only works if Paired-end data has equal length r...
• Barcode Splitter On Paired End Reads
  Dear Galaxy team,   I am sorry for repeatedly asking this question but I would like some feed bac...
• Masking reads that map to two genomes in galaxy
  I've gotten RNAseq data (paired end Illumina) that is from two different species. I've used Topha...
• 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...
• Mapping paired reads to reference genome, variant calling
  I am trying to map a trio of paired-end Illumina reads to a reference genome, then identify polym...