Galaxy tutorial "Differential abundance testing of small RNAs" corrupted


I am working with the MicroRNA differential expression and tested the “Differential abundance testing of small RNAs” tutorial but it was corrupted in many ways.

I even tried with the tutorials own data. but still no result.

you can see the problem in steps such as : Converting bam to fastq, manipulate fastqc and the whole Hands-on: Hierarchical alignment to rRNA and miRNA reference sequences (3) step.
So anyone figure out what is the problem /.?

Hi @amir,

thanks for checking. Which Galaxy instance are you using ( and can you please send an error report for those broken tools? I will have a look then.



I remember last time I did it, there was a missing step on a resulting fastq. The fastq should be groom-ed since they did not show up in the tool next step? (I think it was just after Converting bam to fastq)

i saw this too

There is no error to send , problem is, when you convert fastq to bam :
1: Hisat doesnt recognize the data, and you should change the data type to fastqsanger.gz manually again. because Convert bam to Fastq tool, make Fastq data and not fastqsanger.
2: After Converting, and using hisat2, the result does not has any volume(byte) to work with
I suggest to do it from A to Z. then you will see the problems.
Thank you for your attention