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• Orientation in paired-end sequencing?
  I am new to bioinformatics and currently learning how to use Bowtie 2. As written in the manual: ...
• pair-end, mate-pairs coding
  Hello, recently I received quite big dataset of three pair-end libraries (350, 550, 700 is) and ...
• Can two mates have different file size?
  Hello I wanted to ask if it is possible for two paired files -- from paired end sequencing -- to...
• Determining Paired-end or Mate-pair insert length in De Novo Sequencing
  Hello, I have a few questions regarding mate-pair and paired end sequences: 1. Does one have t...
• Do mate 1 and mate 2 reads correspond to the 5' and 3' ends?
  In a paired-end sequencing experiment, a mate pair is generated. Let's call them read 1 and read ...
• Mate paires alignment
  Hello, I would like to ask how the mate paired reads from sequencing alignment to the reference...
• BAM FLAG mate unmappedand mate reverse strand
  Can anyone please explain in one sentence the meaning of these two flags (mate unmapped and mate ...
• Paired-end reads - what is what?
  This is probably a dummy question, but I haven't found an explanation and I want to be sure. When...
• Difference between mate-pair, paired-end and long read
  Hello everyone, I writing here because I have some questions for you. I wondered what the essent...
• Samtools Mpileup And Overlapping Paired-End Reads
  I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious...
• mate pair trimming ?
  Prior to an assembly, I would like to trim out adaptor sequences from mate pair library. I use u...
• tophat --max-multihits impacts 'mapped in a proper pair'
  Hi everyone, I have a RNA-seq library (paired-end) with a large amount of multimappers because i...
• Qualimap insert size result explanation
  for  Qualimap users what is the meaning of zero insert in the insert size histogram? knowing th...
• Samtools flagstat results
  221372 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 sup...
• Thorough Documentation Of Samtools Flagstat
  I am trying to find thoroughfull documentation of samtools flagstat for every row for file Un.bam...
• Interpreting Flagstat Output
  Hi, This question has probably been asked many times but it is still not very clear to me from w...
• How exactly does MAQ handle mate-pair data
  Hi, I'm trying to align a 3.5K-insert mate-pair library using MAQ 0.7.0. From the man page ([htt...
• Tophat Parameters Misunderstanding
  Hi, I have a little understanding problem on several tophat parameters : -r/--mate-inner-dist ...