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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.Originally posted by westerman View PostComment
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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'.Originally posted by Arupsss View Post
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.Comment
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Miseq Fastq Format: Forward and Reverse Issue
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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