SEQanswers Miseq Fastq Format: Forward and Reverse Issue
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 06-19-2012, 11:17 AM #1 Arupsss Member   Location: Trento, Italy Join Date: May 2011 Posts: 44 Miseq Fastq Format: Forward and Reverse Issue I am doing some experiment with BowTie. Now, I want to do experiment with 150 bps read length. So, I download it from here. There, it is written 1 forward and 151 reverse. Can anybody help me what does this forward and reverse means ?
 06-19-2012, 11:31 AM #2 westerman Rick Westerman   Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104 It is showing you the base at the 5' position. The '1' means that the forward strand begins at position 1. 5' to 3'. The '151' means that the reverse strand ends at position 151 once again reading 5' to 3'. BTW: There is no need to repeat your question in multiple threads. BTW#2. The miSeq puts out 151 base pair reads not 150 bp reads. That is just the way it is.
06-19-2012, 11:49 AM   #3
Arupsss
Member

Location: Trento, Italy

Join Date: May 2011
Posts: 44

Quote:
 Originally Posted by westerman It is showing you the base at the 5' position. The '1' means that the forward strand begins at position 1. 5' to 3'. The '151' means that the reverse strand ends at position 151 once again reading 5' to 3'. BTW: There is no need to repeat your question in multiple threads. BTW#2. The miSeq puts out 151 base pair reads not 150 bp reads. That is just the way it is.
means first end (1-151) is taken from DNA's forward stand and second one (152-302) taken from DNA's reverse strand ? Means are they reverse complement ? Sorry, I have very little idea about Bioinformatics.

06-19-2012, 12:21 PM   #4
westerman
Rick Westerman

Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

Quote:
 Originally Posted by Arupsss means first end (1-151) is taken from DNA's forward stand and second one (152-302) taken from DNA's reverse strand ? Means are they reverse complement ? Sorry, I have very little idea about Bioinformatics.
SRA shows the two reads per pair in what I consider to be a strange manner since SRA combines both reads together despite that there should be a insert distance (positive or negative) between the pairs. But given that view, then yes, 1-151 would be 5' to 3' then it goes in reverse from 3' to 5'.

When you eventually download the reads in fastq or fasta format the 'forward' reads will be 5' to 3' bases 1 to 151. The 'reverse' reads should be 5' to 3' bases 151 to 1. Although, when I download the fastq I am getting 150 bases for the forward and 152 bases for the reverse. So using the SRA tools might be a better choice for data manipulation.

 Tags illumina fastq, miseq