Hi,
I’m having trouble using the tool “footprint” (link to the Galaxy tool: Galaxy).
In the section parameter “chromosome length” it’s requested to input a tab delimited file where in the first column there’s the chromosome number (for example ‘chr1’) and in the second column its corresponding length.
I’ve created such file and then uploaded it in my history. The file is https://usegalaxy.eu/api/datasets/4838ba20a6d86765499a42418c58a431/display?to_ext=tabular .
I attach also a screenshot of how the file is presented on Galaxy:
So, there’s written that the format accepted is a tabular file, but then when I insert one it doesn’t work.
I checked multiple times the file, tried to manipulate it so to make it work, but I didn’t manage to solve the issue.
I don’t understand if it’s a problem related to my file or a problem of the Galaxy tool.
Thanks in advance if someone will be able to help me,
Marianna
Hopefully you discovered this already, but if a tool doesn’t “see” a dataset in the history, and you have already confirmed that the dataset has an accept format, it usually just means that you are in the wrong history.
Go under Data → Histories to check and then toggle to the history with the file, load up the tool form again, and see if that solves the problem.
And, for this tool, it seems the tool is double checking that both the BAM and tabular chrom sizes file are based on the same genome build. That means both should have the same database assignment, too. Your tabular data does have a database. If you also mapped against mm39, your BAM should already have that assigned. UCSC’s Table Browser is one place to get that file directly, using this tool → UCSC main. How-to FAQ: Directly obtaining UCSC sourced *genome* identifiers
Hope this helps, but you can explain more if not!
ps: Avoid dragging and dropping for datasets already in the history if at all possible! I can explain why if interested…
Hi @jennaj , thanks for answering me!
So, first of all, I know to which type of situation you’re referring too (it has happened to me other times), but this is not the case because I was already on the correct history (and in fact it’s shown in the part on the right, where it’s usually situated the current history).
Secondly, about the database assignments, I checked that also the BAM file(s) has the mm39 database assignment and yes it has/they have it.
I leave it here two examples of BAM files to show that there’s the db assignment:
Then finally, I also tried to download the chromInfo file from UCSC, and I’ve also modified so to take only the two first columns (chrom name and size), so to match the indications of tha tab file to insert in this field, but still it doesn’t accept it.
These are the two UCSC files:
Last thing, also if I don’t drag and drop, but I choose the file using the three dots button, it still doesn’t take it, it doesn’t allow me to choose it.
I don’t know really what it could be, everything seems okay to me…
Let me know if there’s anything else I could try or if you think it could be a bug of the tool.
In the meantime, thank you for your help!
Awesome, I didn’t think to check also there.
So, it was an already known bug of the tool, but still it hasn’t been solved…
Thanks a lot, hopefully it will be resolved now that you added new info. I’ll see if it’s necessary to add comments, but for the moment I don’t think so.
Thank you!
