Question: Pooling fastq reads from different samples in metabarcoding
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gravatar for lvogel
21 months ago by
lvogel20
Western Europe
lvogel20 wrote:

Hi, I've read that it is possible to pool all fastq files of Illumina reads, of different samples for metabarcoding, into one file, and then continue with analysis. I've even heard that you can combine reads from other runs, if they are from the same environment. Now, I would think that if you are going to combine samples from different runs, they should also be from the same sequencing depth, or the relative abundance estimations of biological sequences will be all wrong. Could anyone comment? Thanks.

illumina metabarcoding • 600 views
ADD COMMENTlink modified 21 months ago by Pierre Lindenbaum115k • written 21 months ago by lvogel20
3
gravatar for Pierre Lindenbaum
21 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

if you plan to mark the duplicates , reads from different flowcell/lane/library cannot be considered as an optical/pcr duplicate So you'll have to assign a distinct read-group for each of those conditions. Furthermore, tools like BWA use a subset of reads to calculate the average segment length.

ADD COMMENTlink modified 21 months ago • written 21 months ago by Pierre Lindenbaum115k
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