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bgruening - I need to share a history with you - this is the one where when I select multiple datasets it does not give me the option to build a collection. Please DM me the correct email to share with.
btw I tried to get an "overview" of this history using parsec but
parsec -g usegalaxyeu datasets get_datasets --history_id 46051bf8534e30b9 gives me an empty list
Hi all! Would it be possible to run the interproscan data manager on usegalaxy.eu? the database is missing for latest version 5.55-88.0
not sure I can do this tm, but I will try
Hello
I used Import Annadata and loom to process my single cell data
My genes file included 28 thousand gene symbols and ensemble IDs
Now, although the output of this tool is green, the number of genes is considered zero
And in the matrix he created, my genes are not there
what is the reason?
I used Import Annadata and loom to process my single cell data
My genes file included 28 thousand gene symbols and ensemble IDs
Now, although the output of this tool is green, the number of genes is considered zero
And in the matrix he created, my genes are not there
what is the reason?
1 reply
@amini1573: this is hard to say from your description. Did you follow any tutorial?
Did you mapped against the correct reference genome?
What was your mapping statistic?
I see something: https://usegalaxy.eu/apollo/1399918/jbrowse/index.html
yeah some things are showing, but the right panel ui doesn't load for me, usually it means there's out of memory errors or things like that
do you have access to the logs?
and there are only 4 people in your training group registered
maybe the persons have not clicked the TIaaS link?
One BWA job from one person in your TIaaS group is still waiting for one input dataset to be finished
we have 100 of Phich Its running
hi
if I wanna compare miR expression in cancer tissue vs normal its better to analysis miseq or rna-seq?
if I wanna compare miR expression in cancer tissue vs normal its better to analysis miseq or rna-seq?
hahaha thank you for reminding me that I should write that tool (there is a checksum tool in the toolshed but it does sha256, not md5). I actually need a tool to do md5 and as far as I know it is not possible in Galaxy at the moment.
Hi all, is it possible to create a collection of uploaded files within a workflow (which tool if there is one)? Is the "Apply rules" tool functional as a workflow tool? I want to build a workflow for uploaded paired-end RNAseq data and automate the rule-based generation of a paired collection.
one of the turotials in GTN has something for that
I am prepping for running the "Introduction to Genomics and Galaxy" tutorial and I realise that the bed-file datasets no longer have such a link. on the Usegalaxy.eu server.
Click on the Vis button. Do you see then UCSC?
But I realise that there is a blue field above the list of icons
Facepalms
So it is a small design change with the visualisation button leading to the "Visualize" menu but with a blue bar at the top with the links which used to be on the datasets. So it is me not used to design changes :P
Thanks
Hi everybody, I am currently performing an assembly process of a genome produced with reads from the nanopore system. I already performed the assembly using Flye, then the polishing using medaka, which gives me a consensus.fasta sequence. I am trying to get a corrected and chromosome level assembly using ragtag software. First I did the correction, then the scaffold, then the patch, and now I am trying to do the merge. Here in this last step I have the problem, because it does not generate any output result. I tried to use these programs directly on my computer, but I get a message : Fri Sep 23 11:11:26 2022 --- VERSION: RagTag v2.1.0
Fri Sep 23 11:11:26:26 2022 --- WARNING: This is a beta version of ragtag merge
Fri Sep 23 11:11:26 2022 --- CMD: ragtag.py merge ragtag.patch.fasta ragtag.patch.agp ragtag.patch.ctg.agp ragtag.patch.rename.agp
Fri Sep 23 11:11:26 2022 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'.
Fri Sep 23 11:11:26 2022 --- INFO: Building the scaffold graph from the AGP files
Traceback (most recent call last):
File "/home/sequenceur/miniconda3/bin/ragtag_merge.py", line 430, in.
main()
File "/home/sequenceur/miniconda3/bin/ragtag_merge.py", line 362, in main
agp_multi_sg.add_agps(agp_list, in_weights=weight_list, exclusion_set=comp_exclusion_set)
File "/home/sequenceur/miniconda3/lib/python3.9/site-packages/ragtag_utilities/ScaffoldGraph.py", line 606, in add_agps
for ap in self._get_assembly_points(agp, weight):
File "/home/sequenceur/miniconda3/lib/python3.9/site-packages/ragtag_utilities/ScaffoldGraph.py", line 513, in _get_assembly_points.
raise RuntimeError("{} is in {} but not {}.".format(agp_line.comp, agp, self.components_fasta_fname))
RuntimeError: seq00000005 is in /home/sequenceur/genome_assembly/Lguyanensis_filtree/RagTag/patch/ragtag_output/ragtag.patch.agp but not ragtag.patch.fasta.
Now I use galaxy to try to solve this problem, but apparently the result is the same. Can you please guide me?
Fri Sep 23 11:11:26:26 2022 --- WARNING: This is a beta version of ragtag merge
Fri Sep 23 11:11:26 2022 --- CMD: ragtag.py merge ragtag.patch.fasta ragtag.patch.agp ragtag.patch.ctg.agp ragtag.patch.rename.agp
Fri Sep 23 11:11:26 2022 --- WARNING: Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'.
Fri Sep 23 11:11:26 2022 --- INFO: Building the scaffold graph from the AGP files
Traceback (most recent call last):
File "/home/sequenceur/miniconda3/bin/ragtag_merge.py", line 430, in.
main()
File "/home/sequenceur/miniconda3/bin/ragtag_merge.py", line 362, in main
agp_multi_sg.add_agps(agp_list, in_weights=weight_list, exclusion_set=comp_exclusion_set)
File "/home/sequenceur/miniconda3/lib/python3.9/site-packages/ragtag_utilities/ScaffoldGraph.py", line 606, in add_agps
for ap in self._get_assembly_points(agp, weight):
File "/home/sequenceur/miniconda3/lib/python3.9/site-packages/ragtag_utilities/ScaffoldGraph.py", line 513, in _get_assembly_points.
raise RuntimeError("{} is in {} but not {}.".format(agp_line.comp, agp, self.components_fasta_fname))
RuntimeError: seq00000005 is in /home/sequenceur/genome_assembly/Lguyanensis_filtree/RagTag/patch/ragtag_output/ragtag.patch.agp but not ragtag.patch.fasta.
Now I use galaxy to try to solve this problem, but apparently the result is the same. Can you please guide me?