How to make all files joined?

[thh32]

Basically I have 28 files of r1 and r2 data which I want merged. I am planning on using ea-utils fastq-join but am wondering if anyone knows of a way to make a program go through each pair of files joining them and then moving onto the next automatically?

I have heard of for loops and was thinking of trying to write one but know very little so is it possible to get something like this working:

for Library$_read1 and Library$_read2

do fastq-join -p 1 -o Library$_merged

done


That way it could work its way through all the pairs of files using $ so it goes Library1, Library2 etc

Any help would be greatly appreciated.

Thanks,
Tom

[GenoMax]

Tom: Following will need adjustment based on the exact file names you have but example below works for tcshell.

$ ls -1 *.fq
test1_r1.fq
test1_r2.fq
test2_r1.fq
test2_r2.fq
test3_r1.fq
test3_r2.fq

$ foreach i ( `ls -1 *r1* | cut -d"_" -f1` )
foreach? fastq-join $i\_r1.fq $i\_r2.fq -o $i\_merged.fq
foreach? end

For Bash (assuming the same file names above):

$ for A in `ls -1 *r1*`; do fastq-join "${A%%_*}"_r1.fq "${A%%_*}"_r2.fq -o "${A%%_*}"_combined.fq ;done

[volks]

i quite like xargs:

ls -1 *fq | cut -d _ -f 1 | sort | uniq | xargs -I '{}' -P 4 sh -c "echo processing '{}'; fastq-join '{}'_r1.fq '{}'_r2.fq -o '{}'_merged.fq"

.. will run four commands in parallel.

[rnaeye]

I am not sure if I understood your question completely, but if you are doing end to end joining you can simply use Unix cat like below:

cat file1 file2 file3 > combined-files.fastq

[GenoMax]

I am not sure if I understood your question completely, but if you are doing end to end joining you can simply use Unix cat like below:

cat file1 file2 file3 > combined-files.fastq

thh32 wants to use "fastq-join" utility from ea-utils that merges R1/R2 reads using the overlapping ends.

[rnaeye]

Thanks GenoMax. It seems to be a useful tool to have. Best,