How do I count the number of sequences in a FASTA file?
By FASTA format definition, we know that number of sequences in a file should be equal to the number of description lines. So by counting > in file, you can count the number of sequences. This can be done using counting option of the grep with its count option -c .
Which command is used to find count of lines which contains a particular pattern?
grep command
grep command in Unix/Linux. The grep filter searches a file for a particular pattern of characters, and displays all lines that contain that pattern. The pattern that is searched in the file is referred to as the regular expression (grep stands for globally search for regular expression and print out).
How to count sequences in a FASTA file?
So if you want to count the number of sequences contained in a .fasta file, you can easily have it done using the grep command: What this line does is just selecting all the > characters, and then count all their occurrences.
How to count number of reads in a FASTQ file?
We thus need to subtract the line count from it: All the caveats from Simon’s comment apply: this assumes the “simple” FASTQ format, where each record consists of exactly four lines. I think this is true for all files produced by Illumina sequencers and downstream tools.
How are the sequence identifiers represented in FASTQ?
Each sequence is represented by four lines: the first one being a sequence identifier, the second one is the actual sequence, the third line is usually empty and only contains a placeholder +, while the last line contains the sequence quality scores:
How to count number of reads and number of bases?
Next we want to find the fastest way possible to count these, all timings are the average wall-clock time (real) of 10 runs collected with the bash time on an otherwise unloaded system: zgrep . ERR047740_1.filt.fastq.gz | awk ‘NR%4==2 {c++; l+=length ($0)} END { print “Number of reads: “c; print “Number of bases in reads: “l }’