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Old 12-30-2013, 01:45 PM   #6
PhD Student
Location: Denmark

Join Date: Jul 2012
Posts: 164

Originally Posted by arcolombo698 View Post
I have a question the alignment process.

for a given sample, I normally perform quality control on the samples and afterward for a specific sample, I run the alignment on the paired trimmed samples (ie. running the alignments on the entire trimmed fastq files).

Are you suggesting that it is not ideal to run the alignment on an entire fastq file? but a partition of the fastq file? Does it matter if the project is DNA ? or RNAseq?

Thank you.
I am just confused because I normally run the alignments on a complete fastq file, and not a partition of a fastq file.

Is there a resource that you'd recommend?
No, its not an issue if you decide to run the alignment of an entire fastq file against the entire reference sequence.

I was suggesting the preferred way of doing the task in parallel to may be utilize a HPC cluster if you have access to one. You'd rather split the fastq file than split the reference file for parallelism.
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