merging two fastq files from exome sequencing

[rohan_1925]

Hi ,

I have 50 samples,each having paired end reads,Do you know of using "cat" command of merging paired end reads for each sample in one command? for example merging the 2 files below in one command in this post using some regular expression?

http://seqanswers.com/forums/showthread.php?p=127938

Else I have to merge each sample one by one.

Thanks,
Rohan

[GenoMax]

If your file names follow some pattern then you can possibly use a shell script that can "cat" the files for the samples together using a loop. If you post representative example of the names then someone can help you.

Now the question. Why do you want to do this? Most programs do not need the reads to be in a single file (in fact that may cause you problems down the road).

[rohan_1925]

Hi,

Below are some of the samples.

51772BL1_R1.fastq
51772BL1_R2.fastq
51805BL1_R1.fastq
51805BL1_R2.fastq
52451BL1_R1.fastq
52451BL1_R2.fastq


Since,I am new to this kind of analysis and have dealt with very few files till now to set up my workflow, I did the analysis after merging the files only.
Can you elaborate on what kind of problems might come so I can think more on this?


Thanks

[vivek_]

That example is not very helpful since looking at the file names, it appears that each Fwd/Rev fastq file appears to be from a different sample.

You do not want to concatenate those prior to alignment and if you have a HPC cluster where you do the analysis, its much faster to do the alignments on multiple fastq files in parallel and then merge the alignments depending on your workflow.

[maubp]

It is also wise to keep track of the different samples/replicates for later analysis (for example it could be one of these samples/replicates has problems). This is much harder if you start by merging everything (pooling the reads).