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when to merge lane replicates?

Dear all,

I have a set of samples each having multiple lane's replicates. When shall I merge the different replicate? BEFORE (that is, merge the fastq files) or AFTER (that is, merge the BAM files) the alignment?

Does the step of merging varies if the study is WGS or RNAseq?

I haven't found a straight answer on Google, so I am asking.

Thank you

alignment next-gen
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updated by GenoMax GenoMax • written by marongiu.luigi marongiu.luigi

Is this just the same library being loaded on the multiple lanes or are these actually different libraries?

• 1 views • link
written by Devon Ryan Devon Ryan

1 answer

If the same sample ran on multiple lanes as a part of pool you can merge the data at fastq stage (people will tell you to add RG etc., it is your call). Sequencing facilities should use --no-lane-splitting option when using bcl2fastq to avoid this issue.

• 1 views • link
written by GenoMax GenoMax

perfect, thank you! now it is clear

• 1 views • link
written by marongiu.luigi marongiu.luigi

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