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I am new to DNA sequencing and I want to know is there any scripts or tools to count base pairs of a particular sequences. I am working on illumina HiSeq 2000.
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Why would you count base pairs? And what does this have to do with the HiSeq2000? What is your goal? What are you planning to do? -
Actually, I am just a technical research assistant helping out a researcher for some works of him.(means doesn't know much about dna sequencing) He wants that statistics and I can't figure out how to calculate that. I know how to count no. of spots,sequences but stuck in base pairs.Originally posted by sphil View Post
For example,The following run have summary information such as # of Spots and runs. I already trimmed the adaptor sequences and merged the short reads. He wants the statistics of each process.
I use FastQC and other tools to evaluate the sequence data. However,it doesn't provide the function to count base pairs.
Any idea?Comment
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Fastx-quality-stats from the FASTX-toolkit may give what you need.
$ fastx_quality_stats -h
usage: fastx_quality_stats [-h] [-i INFILE] [-o OUTFILE]
version 0.0.6 (C) 2008 by Assaf Gordon ([email protected])
[-h] = This helpful help screen.
[-i INFILE] = FASTA/Q input file. default is STDIN.
If FASTA file is given, only nucleotides
distribution is calculated (there's no quality info).
[-o OUTFILE] = TEXT output file. default is STDOUT.
The output TEXT file will have the following fields (one row per column):
column = column number (1 to 36 for a 36-cycles read solexa file)
count = number of bases found in this column.
min = Lowest quality score value found in this column.
max = Highest quality score value found in this column.
sum = Sum of quality score values for this column.
mean = Mean quality score value for this column.
Q1 = 1st quartile quality score.
med = Median quality score.
Q3 = 3rd quartile quality score.
IQR = Inter-Quartile range (Q3-Q1).
lW = 'Left-Whisker' value (for boxplotting).
rW = 'Right-Whisker' value (for boxplotting).
A_Count = Count of 'A' nucleotides found in this column.
C_Count = Count of 'C' nucleotides found in this column.
G_Count = Count of 'G' nucleotides found in this column.
T_Count = Count of 'T' nucleotides found in this column.
N_Count = Count of 'N' nucleotides found in this column.
max-count = max. number of bases (in all cycles)Comment
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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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