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.
-
-
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
-
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
-
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment