NGS Qc: MultiQC not recognizing FASTQC raw results from list

Question: NGS Qc: MultiQC not recognizing FASTQC raw results from list

8 months ago by

Hi,

I am trying to aggregate results from FAST Qc lists by MultiQC, but MUltiQC isnt recognizing the list . I have tried to verify the accepted format (txt), but to no avail. Also, Trimmomatic is throwing up error message (but still works).

I have multiple bam files from single cell RNA-Seq data data analysis, will mergigng all these bam files will be helpful in downstream processing? (for the creation of an expression matrix) Any suggestions will be helpful. Thanks.

list fastqc multiqc collection bam • 401 views

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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by rajeev.vikram • 0

8 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

These functions are working at https://usegalaxy.org. This is a graphic for using MultiQC on FastQC output (in a dataset collection of BAMs, with collection type = LIST): https://imgur.com/a/zdq8L

Help for using collections with FastQC is specifically covered in this tutorial (NGS logistics): https://galaxyproject.org/tutorials/ngs/

With full Dataset Collection operations covered in this tutorial: https://galaxyproject.org/tutorials/collections/

Many other Galaxy tutorials make use of collections in example analysis workflows. Please see all Galaxy tutorials here: https://galaxyproject.org/learn/

If you are working somewhere else (not at Galaxy Main https://usegalaxy.org), and the functions are not working as expected when using the methods described above, contact the administrators of that server to find out more. There could be a server-side issue. Contact information is usually included on the landing page of the server, but some public servers also have contact information here: https://galaxyproject.org/public-galaxy-servers/

Thanks! Jen, Galaxy team

ADD COMMENT • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k

I am sorry but, MultiQC is still not working as desired and now there seems to be a problem with the server. I cant log out of my account (message: Failed to authorize action.)and many analysis programmes are queued but not running (for quite a long time). I am using the main server.

ADD REPLY • link modified 8 months ago • written 8 months ago by rajeev.vikram • 0

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