visualization.html can't be loaded

[lida-R]

Hi there,

I used below script to run miRge3.0 pipeline and after it generates the interactive visualization html file "miRge3_visualization.html" I can open it but nothing loaded!
miRge3.0
-s $samples
-db miRBase
-lib /TOOLS/miRge3_Lib
-on human
-cpu 20
-gff
-trf
-nmir
-dex
-mdt /miRge3_PIPELINE/MetaData_mirge3.csv
-a AACTGTAGGCACCATCAAT --qiagenumi -umi 0,12
-q 20 -m 16 -NX -minl 16 -maxl 25 -c 2 -tcf -udd
-mloc 3 -sl 25 -olc 14 -clc 30
-o miRge3_PIPELINE \

Attached is what I see when open the html file:

[arunhpatil]

Hi @lida-R,

If you downloaded this html file from a server then you should also download the index.js file from the server too. When placed togather, the html file reads JS and loads the data. Also, can you try one of the test samples provided here (https://mirge3.readthedocs.io/en/master/quick_start.html#cli-example-usage), and see if you can visualize?.

Let me know how it goes.

Thank you,
Arun.

[lida-R]

Hi Arun,

Thank you for your reply.
I copied index_data.js and miRge3_visualization.html files in the same folder but still didn't work.
I tried the test script and test sample and that html works. (Works in Edge not chrome)
I'm not sure if something is wrong with my script?

Here is the test script I ran and it worked:

miRge3.0 -s SRR772403.fastq.gz -lib /bioinfo/share/TOOLS/miRge3_Lib -a illumina -on human -db mirbase -o /bioinfo/PROJECTS/SMALL_RNA/TEST -gff -cpu 16

Here is my script that didn't work:

miRge3.0
-s $samples
-db miRBase
-lib /TOOLS/miRge3_Lib
-on human
-cpu 20
-gff
-trf
-nmir
-dex
-mdt /miRge3_PIPELINE/MetaData_mirge3.csv
-a AACTGTAGGCACCATCAAT --qiagenumi -umi 0,12
-q 20 -m 16 -NX -minl 16 -maxl 25 -c 2 -tcf -udd
-mloc 3 -sl 25 -olc 14 -clc 30
-o miRge3_PIPELINE \

Thank you for your help,
Lida

[arunhpatil]

Hi @lida-R,

Can you tryout just one sample instead of $samples and make a simple run for the purposes of testing. However, if you have read counts (Counts.csv or RPM.csv files) then please investigate them. If they seem fiine, then there is some issue with visualization and it should not affect the end results as such.

I recommend you try and test the command with few parameters and check if the result summary can be visualized.

miRge3.0
-s $samples
-db miRBase
-lib /TOOLS/miRge3_Lib
-on human
-cpu 20
-a AACTGTAGGCACCATCAAT --qiagenumi -umi 0,12
-udd
-o miRge3_PIPELINE

I can check if the qiagen UMI parameters are correct for your samples. If you could share a subset of your sample via google drive at my gmail arun26feb or anyother secure platforms, I can take a look.

Thank you,
Arun.