Question: combining indexed paired reads from two lanes of a Hiseq rapidrun
gravatar for mduffy
4.4 years ago by
mduffy0 wrote:


I am doing paired end RNAseq, I have a single multiplexed pool that was run over both lanes of a Hiseq rapidrun, thus for each indexed sample I have two forward reads and two reverse reads.

For a single index is there a way I can combine the two sets of forward reads from the different lanes and separately combine the two sets of reverse reads from the different lanes whilst maintain the pair identification so that they will still map as concordant pairs by tophat2?


ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by mduffy0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


With the assumption that the .fastq sequence identifiers are unique across both samples (should be by default with this technology - the lane will differ in the IDs), you can simply concatenate the forward reads together and do the same for the reverse, then proceed with QA/QC and downstream steps. The tool to use is "Text Manipulation -> "Concatenate".

If there are any complicating factors, please share a data sample and more details. There are methods to rename sequences.

Best! Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k

Hi Jennifer/ team

What if it is the custom reference genome to be indexed from history? What I mean is, for example, MYREFGENOME is represented by 4 fastq files (paired end reads from 2 lanes). How should we deal with all the files so we can use MYREFGENOME with downstream aligners? The difficulty is in the two separate lanes (not paired end reads). Mine is WGS data.

Kindly clarify if you or anyone can help. Thank you.

ADD REPLYlink written 18 months ago by bhao.haob0
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