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Currently, the pipeline considers as a biological replicate any sample which has the same id under the sample column of the samplesheet followed by a different suffix determined by an underscore e.g.:
sample1_r1
sample1_r2
sample2_r1
sample2_r2
This information is used by the pipeline in this code line to determine whether multiple groups are present e,g, sample1 and sample2 in the example above and whether replicates exists r1 and r2 also using the example above.
However, the problem with this approach is that is based on the sample names and sometimes this can be problematic since depends on the correct naming of the replicates with the underscore, see this issue.
I guess that the solution to this problem will be to include again the replicate column into the samplesheet, although this information is currently only used for enabling the run of DESEQ2_QChere and MACS2_CONSENSUShere.
I would like to know your opinion here @drpatelh, @bjlang and any other willing to give feedback of course :smi
The text was updated successfully, but these errors were encountered:
JoseEspinosa
changed the title
Provide replicate information explicitely in samplesheet
Provide replicate information explicitly in samplesheet
Jun 21, 2023
I'm not sure if there has been any input on this, but we have several ChIP-Seq projects that have biological reps, so having some way to keep track of these and perform IDR would be great.
Description of feature
Currently, the pipeline considers as a biological replicate any sample which has the same id under the
sample
column of the samplesheet followed by a different suffix determined by an underscore e.g.:This information is used by the pipeline in this code line to determine whether multiple groups are present e,g,
sample1
andsample2
in the example above and whether replicates existsr1
andr2
also using the example above.However, the problem with this approach is that is based on the sample names and sometimes this can be problematic since depends on the correct naming of the replicates with the underscore, see this issue.
I guess that the solution to this problem will be to include again the
replicate
column into the samplesheet, although this information is currently only used for enabling the run ofDESEQ2_QC
here andMACS2_CONSENSUS
here.I would like to know your opinion here @drpatelh, @bjlang and any other willing to give feedback of course :smi
The text was updated successfully, but these errors were encountered: