Difference between total number of reads in fastq file and no of bases/nt sequences in fastq file?
Hello there; I am a beginner in Data analysis domain and want to clear my concept number of reads and no of bases in fastq file.
what is the difference between total number of reads in fastq file and no of bases/nt sequences in fastq file?
what command will return out put for total number of reads and total no of bases?
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Each read represents a short piece of DNA that was sequenced. Reads consist of a certain number of bases. When you add up all the bases from all the reads, you get a total number of bases.
There is a program called stats.sh
from the BBtools package that will tell you the number of reads (it will call them scaffolds/contigs) and a total number of bases in each fastq files:
Minimum Number Number Total Total Scaffold
Scaffold of of Scaffold Contig Contig
Length Scaffolds Contigs Length Length Coverage
-------- -------------- -------------- -------------- -------------- --------
All 1,000 1,000 149,982 149,981 100.00%
100 1,000 1,000 149,982 149,981 100.00%
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