This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Can we concatenate two fastq files from same sample but different runs

Hi,

I have two paired end file sets for a sample.

Forward: sample_R1_001.fastq.gz, sample_R1_002.fastq.gz

Reverse sample_R2_001.fastq.gz, sample_R2_002.fastq.gz

This is not a multilane case. They were two separate runs from the same sample aliquot!!

  1. Should I concat R1_001 and R1_002 fastq files ?
    1. Or should I run them as two separate pipelines?
    2. Or should I run them separately till alignment and then do BAM merge like for multilane samples?

Thanks, Payal

sequencing rna-seq
• 5,934 views • link
updated by anamaria • anamaria • written by Payal Payal

Whether a separate run or separate lane makes little difference, they are still technical replicates. They should not be merged.

• 1 views • link
written by BioinfGuru BioinfGuru

Whether a separate run or separate lane makes little difference, they are still technical replicates. They should not be merged.

I have not seen any lane practical lane effects. Illumina offers a --no-lane-splitting option for their post processing software (bcl2fastq) which will make a single file per sample, if the same pool ran across multiple lanes of a flowcell.

• 1 views • link
written by GenoMax GenoMax

s/should not be/should be/

• 1 views • link
written by Devon Ryan Devon Ryan

But is this the case also for variant calling? I remember in GATK they take care for lane in their analysis (case of de-multiplexed).

However, if you are generating multiple libraries for each sample, and/or multiplexing samples within and/or across sequencing lanes, the data must be de-multiplexed before pre-processing, typically resulting in multiple sets of FASTQ files per sample all of which should have distinct read group IDs (RGID).

• 0 views • link
written by Medhat Medhat

There are no appreciable lane effects any more so they have nothing to adjust.

• 0 views • link
written by Devon Ryan Devon Ryan

1 answer

If I am not wrong, --no-lane-splitting is only available for bcl2fastq2, not for the bcl2fastq.

• 0 views • link
written by anamaria • anamaria

Log in to answer this question.

More posts like this