Question: when to merge lane replicates?
0
gravatar for marongiu.luigi
6 months ago by
Germany, Mannheim, UMM
marongiu.luigi340 wrote:

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

next-gen alignment • 230 views
ADD COMMENTlink modified 6 months ago by genomax59k • written 6 months ago by marongiu.luigi340

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

ADD REPLYlink written 6 months ago by Devon Ryan86k
1
gravatar for genomax
6 months ago by
genomax59k
United States
genomax59k wrote:

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.

ADD COMMENTlink modified 6 months ago • written 6 months ago by genomax59k

perfect, thank you! now it is clear

ADD REPLYlink written 6 months ago by marongiu.luigi340
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