How not to merge R1 and R2 pair-end files in multiqc report

Question

[poecile.pal]

Good morning,

Could you please advise how to generate multiqc report without merging R1 and R2 pair-end files?

My files look like H_SAMPLE2_S29.trim_fin.R1_fastqc.zip, H_SAMPLE2_S29.trim_fin.R2_fastqc.zip. Multiqc generates H_SAMPLE2_S29 stats in the report. But I expect to have stats for R1 and R2 separately.

v1.12 and v1.14 versions give the same result. I have tried --file-list, but it didn't help. I also tried to rename zips, but, as I understand it, renaming the contents of the files in zips is required. Maybe there is an easy way to set a specific multiqc flag? --fn_as_s_name doesn't lead to the desired result.

Thank you in advance!

Best regards,
Poecile

[SushiRoll]

Hi Poecile,

Isn't that what multiqc is supposed to do? Maybe you should run fastQC to get separate results.

[poecile.pal]

SushiRoll,

Thanks for the answer!

I use multiqc to combine the results obtained by fastqc (yes, fastqc reports folder contains reports for R1 and R2 separately: H_SAMPLE2.trim_fin.R1_fastqc.zip, H_SAMPLE2.trim_fin.R2_fastqc.zip).

multiqc generates the report with tables and graphs in which the individual units are rows like H_SAMPLE1, H_SAMPLE2. For example, %GC for H_SAMPLE1, %GC for H_SAMPLE2. I would like to see %GC separately for H_SAMPLE 1.R1 and H_SAMPLE1.R1, H_SAMPLE2.R1 and H_SAMPLE2.R2 in the final table. But multiqc automatically combines paired samples.

Answer 1

[Phil Ewels]

It's because you have _trim in the filenames before the _R1 bit. MultiQC is "cleaning" the sample names back to this, which makes them identical and overwrite one another.

To fix this you can:

• Change the filenames to move the _R1 bit earlier in the filename (then rerun FastQC and MultiQC)
• Stop MultiQC from cleaning any sample names with the --fullnames flag (see docs)
• Customise MultiQC cleaning patterns to remove the _trim string (see docs)

[poecile.pal]

Phil Ewels,

Thank you so much for your help!

It was too long for me to rerun fastqc due to the large number of samples, so, I renamed all archives and then their contents:

unzip SAMPLE11_R1_001_trim_fin_fastqc.zip && cd SAMPLE11.trim_fin.R1_fastqc && sed -i 's/\.trim_fin\.R1\.fastq\.gz/_R1_001_trim_fin_fastqc\.gz/' summary.txt && sed -i 's/\.trim_fin\.R1\.fastq\.gz/_R1_001_trim_fin_fastqc\.gz/' fastqc_data.txt && sed -i 's/\.trim_fin\.R1\.fastq\.gz/_R1_001_trim_fin_fastqc\.gz/' fastqc_report.html && cd .. && rm SAMPLE11_R1_001_trim_fin_fastqc.zip && zip -r SAMPLE11_R1_001_trim_fin_fastqc.zip SAMPLE11.trim_fin.R1_fastqc && rm -r SAMPLE11.trim_fin.R1_fastqc

(and similarly for other files)

Indeed, multiqc separated paired samples.

But, of course, it's not very convenient) So I have tried using the flag --fullnames, and it works!

Thanks again!