Concatenate Paired End Reads Files In Order

[lala2013]

Hi, I wanted to combine paired end reads into two files--one for R1 and one for R2. How do I do it using Linux Command line while making sure the orders are the same in the two file files?

For example, here are all the files in the directory
L001_R1_001.fastq
L002_R2_001.fastq
L004_R1_001.fastq
L005_R2_001.fastq
L001_R2_001.fastq
L003_R1_001.fastq
L004_R2_001.fastq
L006_R1_001.fastq
L002_R1_001.fastq
L003_R2_001.fastq
L005_R1_001.fastq
L006_R2_001.fastq

I wanted to do the following:
cat L001_R1_001.fastq L002_R1_001.fastq L003_R1_001.fastq L004_R1_001.fastq L005_R1_001.fastq L006_R1_001.fastq > R1.fastq

cat L001_R2_001.fastq L002_R2_001.fastq L003_R2_001.fastq L004_R2_001.fastq L005_R2_001.fastq L006_R2_001.fastq > R2.fastq

I can manually sort, copy, and paste for now. But what is a good way of doing it for large number of samples?

Thanks

[kcchan]

The quick and dirty way would be

cat *R1* > R1.fastq
cat *R2* > R2.fastq

[lala2013]

Can you make sure the two output files combined the input files in the same order, like L001-L006?

[winsettz]

Can you make sure the two output files combined the input files in the same order, like L001-L006?

[m@f ~]$ head 1
1
[m@f ~]$ head 2
2
[m@f ~]$ head 3
3
[m@f ~]$ cat 1 2 3 | head
1
2
3
[m@f ~]$ cat 2 1 3 | head
2
1
3

In short, doing

cat L001 L002 L003 L004 > filename

If you feel fancy with for-loops:

for SUFFIX in R1_001.fastq R2_001.fastq
do
cat L001_$SUFFIX L002_$SUFFIX L003_$SUFFIX L004_$SUFFIX L005_$SUFFIX L006_$SUFFIX > cat_$SUFFIX
done