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Processing ddRAD reads
Navigate to exercise location
cd intro_to_rad_2018/demultiplexing/process_ddRAD_stacks
Investigate reads. We paid the sequencing facility for 50,000 paired end reads.
How can be confirm we got this?
#we have two fastq files
ls -lh *.fastq
#take a look at the top of the files
less Lib01_R1.fastq
#how long are the reads?
#type 'q' to exit
#how many lines are in each fastq file?
wc -l Lib01*.fastq
#look at how many reads there are (note that fastq generally files have 4 lines per read)
expr $(cat Lib01_R1.fastq | wc -l) / 4
expr $(cat Lib01_R2.fastq | wc -l) / 4
Paired end read files should have matching names read for read.
Double-check this is case for your reads
#this can be checked many ways, here is one option:
#search for lines that start with @ symbol (the read definition lines in our fastqs)
#and save the top 10 of them as a text file.
#Repeat for the R2 reads.
#Then line them up
grep "^@" Lib01_R1.fastq | head > first_10_R1_read_names.txt
grep "^@" Lib01_R2.fastq | head > first_10_R2_read_names.txt
paste first_10_R1_read_names.txt first_10_R2_read_names.txt