Hi, I have a question about fastq and fastq.gz files. I understand that fastq.gz is the compressed version of fastq file. Can I combine all the R1.fastq.gz files and R2.fastq.gz separately before feeding it to fastQC ? Thanks.
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Looks like fastqc will use one thread per file. Reading the -help for fastqc it states --threads "Specifies the number of files which can be processed simultaneously". Perhaps upping --threads to equal the number of fastq you have, then giving it all the fastq as inputs is the way to go? Going divide-and-conquer is what you need to do.
The problem with cat'ing all your fastq is that the statistics would be calculated as average of all reads: you might not catch an anomaly in one subset of reads, especially if it gets averaged out by the other three set of reads.Last edited by winsettz; 10-15-2013, 12:00 PM.
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Originally posted by lala2013 View PostSorry I didn't make it clear. Is it possible to do the following and feed R1.fastq.gz to fastQC?
cat L001_R1.fastq.gz L002_R1.fastq.gz L003_R1.fastq.gz L004_R1.fastq.gz > R1.fastq.gz
Code:zcat L001_R1.fastq.gz L002_R1.fastq.gz L003_R1.fastq.gz L004_R1.fastq.gz | gzip -c - > R1.fastq.gz
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Originally posted by vivek_ View PostI think cat does concatenate gzipped files. You don't need to gzip again either.
O.K. I just went to the FastQC site and under the Change Log:
3-5-12: Version 0.10.1 released
Added a workround to allow the analysis of concatenated gzipped files(emphasis mine)
Fixed a bug when FastQC was installed in a path containing characters needing to be escaped in a URL
Added an option to specify the location of the java interpreter on the command lineLast edited by kmcarr; 10-15-2013, 01:33 PM. Reason: Should have read the release notes before posting
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