I didn't intend to revive this thread, but as I was searching for a solution to automatize the fastq read counting process, this solution may come in handy to some :
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for i in `find . -name "*.fastq"`; do echo "$i" >> project_nbread.txt; egrep -c "`head -n 1 $i | awk -F '[@:]' '{ print $2 } '`" $i >> project_nbread.txt ; done
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In the case of only one file, you can use this :
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egrep -c "`head -n 1 file.fastq | awk -F '[@:]' '{ print $2 } '`" file.fastq
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This solution will count the number of lines where the id is found in the header of a fastq seq, i.e the number of fastq reads.