Diff command on two Fastq.gz files

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# 1  
Old 11-26-2013
Diff command on two Fastq.gz files


I have to compare two different fastq.gz files that I concatenated, and then zipped into a new merge fastq.gz file.

The files that need to be merged are:
Sample-136-P_S7_L001_R1_001.fastq.gz and Sample -136-P_S7_L002_R1_001.fastq.gz

They were meged to a new file called:

The command entered in Linux was (And this was completed successfully)
 zcat CHLA-136-P_S7_L001_R1_001.fastq.gz CHLA-136-P_S7_L002_R1_001.fastq.gz | gzip > CHLA-136-P_S7_R1.fastq.gz

Now I want to use the diff command to compare the two separate files with the combined file to measure any errors within the merge.

diff <(zcat CHLA-136-P_S7_L001_R1_001.fastq.gz CHLA-136-P_S7_L002_R1_001.fastq.gz) <(zcat CHLA-136-P_S7_R1.fastq.gz)

however this gives me the error ::: "Missing name for redirect".

How can I use the diff command on these two separate files with the concatenated file ?

Thank you!!

Last edited by Don Cragun; 11-26-2013 at 09:55 PM.. Reason: Add CODE and ICODE tags.
# 2  
Old 11-27-2013
There are VERY, VERY likely NO errors in the merge because gzip, zcat, etc., do a checksum.

A better verification if you honestly do not understand what compression does:
(gunzip -c file1.gz; gunzip -c file2.gz)> tmp1; gunzip -c bigfile > tmp2
diff tmp1 tmp2
rm tmp1 tmp2

gunzip -c is the same as zcat....
If compression had problems everyone would be doing diffs, and probably not using gzip, gunzip for anything.
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