Combining qualimap results

[Amy Houseman]

Hello!

I was wondering if it is possible to combine results from samples for easy viewing, something like multiqc but for the qualimap results.

Thanks!

Amy

[Konstantin Okonechnikov]

Hi Amy,

exactly for this purpose there MulitBAMQC mode in Qualitmap, it allows to merge results:

http://qualimap.conesalab.org/doc_html/analysis.html#multi-sample-bam-qc 

Moreover, MultiQC also supports Qualimap, it's provided in the documentation:

https://multiqc.info/docs/#configuring-multiqc 

Best regards,

   Konstantin

 

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[Heather Peng]

Hi Konstatin,

I tried to qualimap multi-bamqc -d /results.tsv -outdir /home/sealight1999/comparison -outformat PDF
But it keep returning :
"Checking input paths

Failed to run multi-bamqc
java.lang.RuntimeException: The raw data doesn't exist for sample: AS_04N_S11_du_stats
Folder path:/home/sealight1999/ASC_lifted/AS_04N_S11_du_stats
Please check raw data directory is present.

        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.checkInputPaths(MultisampleBamQcAnalysis.java:745)
        at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run(MultisampleBamQcAnalysis.java:85)
        at org.bioinfo.ngs.qc.qualimap.main.MultisampleBamQcTool.execute(MultisampleBamQcTool.java:168)
        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190)

        at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:113)"
Inside the results.tsv are three columns : Sample, File Path (to BamQC txt file) and Group.
I realize that multiqc actually provide different information and I'd really like to see the PCA result, is there a way to fix this?
Thank you for your time!

Best regards, 

Heather

[Konstantin Okonechnikov]

Hi Heather,

according to the error, it seems that there are some issues with input or configuration. 

Did you try to run Qualimap MulitQC  on the shared test data:

http://kokonech.github.io/qualimap/samples/gh2ax_chip_seq.zip 

Did everything go well? 

If you share your config and input data I can inspect them. 

Best regards,

   Konstantin

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[Heather Peng]

Hi Konstantin,

Thank you so much for providing the demo data!! It gave me much clearer insight into what was wrong with my data structure.

However, I did noticed that there are various text files inside raw_data; But how are they generated?
besides genome results .txt , I have no  idea how the rest text files come from?

Thank you !!

Best regards,

Heather

Konstantin Okonechnikov 在 2024年6月12日 星期三凌晨12:26:21 [UTC+8] 的信中寫道：

[Konstantin Okonechnikov]

Hi Heather,

these input reports are generated from BAM QC mode, when it's applied with HTML format. Simply it will be located within the corresponding BAM QC report folder together with HTML file and raw report. Alternatively you can use BAM files as input. This is also described in the documentation:  http://qualimap.conesalab.org/doc_html/analysis.html#multi-sample-bam-qc 

Let me know if you have any additional questions.

Best regards,

   Konstantin

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