Question: Forward and Reverse reads from paired end sequencing
gravatar for wormlabnbrc
21 months ago by
wormlabnbrc0 wrote:

The fastq dataset we have after illumina whole genome sequencing is in the form of two files - forward and reverse reads. The forward fastq and reverse fastq must be given separately for bwa right? What happens when we concatenate the forward reads and the reverse reads - does that make any sense?

After illumina paired end sequencing, we are following the Cloudmap: Hawaiian Variant Mapping Workflow for analysis.

Thanks for addressing our queries.

Best Regards, pankajam

bwa galaxy • 1.4k views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by wormlabnbrc0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Yes, for the BWA tools wrapped for Galaxy, the forward and reverse reads are expected to be in distinct datasets and entered that way on the tool form.

Concatenate means to place one file on top of the other (stack the content). This would create a single dataset that would probably run through the tool, but the results would not be optimal (permit the informational use of the paired-end mapping placements).

If you mean instead that the sequences will be either joined end-to-end or assembled (when there is overlap), there are use cases for that but I don't think it is part of the cloudmap workflow/excepted inputs. However, if you have questions about these tools/workflows, the authors take questions - see the links near the bottom of the tool forms.

More about the types of NGS reads in detail to better understand the content:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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