https://usegalaxy.eu status: https://stats.galaxyproject.eu Forum: https://help.galaxyproject.org
@bgruening A tutorial for MD simulation of lysozyme in water is present. But an MD simulation workflow of protein and ligand together is absent. My team is working on creating a workflow. This is essential to fight against COVID-19. If anyone wishes to join our team are also welcome.
in the meantime, if you want to share your workflow we'd be happy to check it
Looking forward for your tool
By the mean time, I have a question the merge tool which has been created is for merging itp file of ligand into top file of protein. How to merge the gro file of ligand and protein which is also a necessary part? Should we explore on creating tool itself for this ?
@dkbryant513 yes, either https://gitter.im/usegalaxy-eu/Lobby or better even https://help.galaxyproject.org/
I'm the original author of MiModD and I'm reading posts in those two places regularly, but not here usually.
@dkbryant513 for your specific last question: You can use MiModD with bowtie2 as the reads aligner as long as you follow the advice at https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/
I'm the original author of MiModD and I'm reading posts in those two places regularly, but not here usually.
@dkbryant513 for your specific last question: You can use MiModD with bowtie2 as the reads aligner as long as you follow the advice at https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/
@bgruening Ok, but i see the bowtie2. But i can't find it in Galaxy MimodD Tool list, not the local MimodD. Because i use the MimodD in Galaxy but local. I see the MimodD read ailgnment tool in Galaxy in this example step 1: https://mimodd.readthedocs.io/en/latest/tutorial_example1.html#ex1-step0 . Now i can not find it in same way. Thank you
@dkbryant513 The Read Alignment tool of the MiModD tool suite is just a bundled aligner that ships with MiModD to make life easy for users of local installs. Bowtie2, OTOH, is a very good aligner that can fully replace MiModD's bundled alignment tool, but is NOT a part of the MiModD tool suite.
If you want to use bowtie2 in a local Galaxy you have to install it separately. Public servers, OTOH, typically have bowtie2 installed anyway, and that's why they are not offering MiModD's own aligner.
If you want to use bowtie2 in a local Galaxy you have to install it separately. Public servers, OTOH, typically have bowtie2 installed anyway, and that's why they are not offering MiModD's own aligner.
I want to know if the my C.elegans WGS data.Fastq from uploaded is missing metadata? so that I decide whether I need to use MiModD Reheader to add the metadata after converting the fastq file to bam, like this step 0 in https://mimodd.readthedocs.io/en/latest/tutorial_example3.html. And, I did not sequence N2 in the experiment, so there is no N2_proof_of_principle.bam file similar to above link step 0, so do I need to use MimodD Reheader in above link step 0.
@praveenkumarpgiindia we are working on a tutorial at the moment, will share it when it is complete
Sharing the workflow. Made by our team with tools available. Inputs welcome
@dkbryant513 You did read https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/ right?
bowtie2 does not take bam as input format. You need to use fastq and that never has metadata. You set RG-ID and sample name in bowtie2.
Hello, why can't I find SnpEff Variant effect and annotation in Galaxy? Like this link:https://sourceforge.net/p/mimodd/wiki/MiModD%20on%20public%20Galaxy%20servers/
@dkbryant513 it's a search issue, the tool is here: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
Hi -- when I attempt to FTP to usegalaxy.eu at ftp.usegalaxy.eu there is a warning about an insecure connection >> Status: Insecure server, it does not support FTP over TLS. Is that the correct URL (same as shown in Upload tool at EU)? Or should a different URL be used right now? Or, avoid FTP and just use file-browsed upload?
The login is not working because of mixing up the account credentials and FTP URL for the target server, but I wasn't sure what the proper URL was right now, or if secure FTP was enabled or not at EU. Thanks!
We have currently this site here for information: https://galaxyproject.eu/ftp/
I'm in contact with the local compute center to figure out if it is the storage or the network.
thanks for your feedback
@bgruening was sind denn "optical duplicates" ?
If I don't have replicates for example, I can switch to the old version of Deseq2. But will be the results different between this two version?
you can not analyse your data with DESeq2 if you have no replicates, also not with older version of DESeq2
