Compare both reads of sample
Entering edit mode
9 months ago
Pratiksha • 0

Hi , I have 4 fastqc folders - seq1_R1, seq1_R2 , seq2_R1, and seq2_R2 which containsfastqc_data.txt. from that file I have to write a program to check if total numer of sequence from seq1_R1 matches with seq1_R2 or not , quality of reads is >50 < 60 . I am stucked how can i do this . i tried this using grep command :

awk '{if (/%GC/ && $2 < 50) { print"GC content is low" } else if (/%GC/ && $2 > 60) { print"GC content is high" }}' ~/data/*_fastqc/fastqc_data.txt

but it is giving me result for every file as an individual file but i need to compare R1 with R2 how can i do this .

Thanks in advance

fastqc_report.txt fastqc • 189 views

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