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    郭哥一说
    @Guogeyishuo_twitter
    mapping rate I can find in the stat of Bowtie2
    郭哥一说
    @Guogeyishuo_twitter
    They have the per base quality score and per sequence quality score,but they don't have an overall mean score.
    James Hong
    @jmshng_twitter
    @bgruening hey Bjorn, do you know if samtools mpileup is supposed to be taking two days to run? i also tried mpileup and it resulted in files that were like 724 GBs in size, which was shocking
    @bgruening username is yunners
    bgruening
    @bgruening:matrix.org
    [m]
    @jmshng_twitter: is still running and has already produced a file of 1,5TB
    what are you trying to do, this does not look healty
    James Hong
    @jmshng_twitter
    @bgruening:matrix.org so im trying to call all the variants
    @bgruening:matrix.org following the GIREMI protocols, they told me to remove dups in my merge bams (paired end), and then run samtools mpileup
    Milad Miladi
    @mmiladi
    hello, I get this error poped up in the html interface by executing extract dataset from a list:
    The server could not complete the request. Please contact the Galaxy Team if this error persists. Error executing tool with id '__EXTRACT_DATASET__': 'str' object has no attribute 'copy'
    
    {
        "history_id": "fb9f7c937f67acb2",
        "tool_id": "__EXTRACT_DATASET__",
        "tool_version": "1.0.0",
        "inputs": {
            "input": {
                "values": [
                    {
                        "id": "87e9199a3df3a6b9",
                        "hid": 202,
                        "name": "assigned reads - read IDs",
                        "src": "hdca",
                        "tags": [
                            "name:calu_fr",
                            "name:subsampling",
                            "name:hg38",
                            "name:fan66494_pass_9329137c_pass.fastq",
                            "name:calu_fr",
                            "name:subsampling",
                            "name:hg38",
                            "name:fan66494_pass_9329137c_pass.fastq"
                        ]
                    }
                ],
                "batch": false
            },
            "which|which_dataset": "first"
        }
    }
    rgilsbach
    @rgilsbach
    Hi, I`m not able to copy the the content of folders from the data library into a history anymore. Until recently this was even possible with data inside of sub-folders. Would be great to enable this function again.
    rgilsbach
    @rgilsbach
    Problem solved - just took ages until the first data appeared. Files outside of folders were fast.
    MzwaneleN
    @MzwaneleN
    Hi. Anybody experiencing jobs being queued for a long time?
    Björn Grüning
    @bgruening
    @MzwaneleN thanks for reporting
    jobs should start soon
    MzwaneleN
    @MzwaneleN
    @bgruening All good now, thank you
    James Hong
    @jmshng_twitter
    @bgruening any idea about mpileup? it is still running - username yunners :(
    Milad Miladi
    @mmiladi
    Some of my Tombo jobs are still gray since yesterday evening.
    Milad Miladi
    @mmiladi
    The message is This is a new dataset and not all of its data are available yet though the input data jobs are finished for long
    Gianmauro Cuccuru
    @gmauro
    I restarted two of your jobs. Is it better, now?
    Milad Miladi
    @mmiladi
    Thanks Gianmauro, I also resubmitted my jobs and they finsihed quickly.
    QZ1130
    @QZ1130
    Hello All, I have a sample question. After I got the analyzed data from deseq2 in R. I want to filter based on log2 FC and padj. Then I type: res_filtered <- results(dds,alpha=0.05, lfcThreshold=1, altHypothesis="greaterAbs") . But there is no changing... Did I miss some fuction so that I can't have it run?
    MzwaneleN
    @MzwaneleN
    @QZ1130 try this: DEGs_DESeq2=res[!is.na(res$padj) & (res$padj)<0.05 & abs(res$log2FoldChange)>=1,]
    Lucille Delisle
    @lldelisle

    Hi,
    Would an admin mind to send me the command line associated to

    History Content API ID     
    11ac94870d0bb33a845bcd65f5015891
    Job API ID:     11ac94870d0bb33aef23f220a40debc5

    The parameter --yAxisLabel does not seem to be updated but I don't know if it comes from the wrapper or deeptools plotHeatmap...

    Jennifer Hillman-Jackson
    @jennaj
    Question at Galaxy Help about how FTP is configured at https://humancellatlas.usegalaxy.eu/. Would someone have time to get back to them? Thanks! https://help.galaxyproject.org/t/why-has-the-ftp-upload-link-disappeared/5736
    Gianmauro Cuccuru
    @gmauro
    @jennaj I replied on Help
    James Hong
    @jmshng_twitter
    is there a package on galaxy for rna editing?
    like GIREMI or REDITools?
    Arthur Eschenlauer
    @eschen42
    @bgruening:matrix.org @erasche I think that I'm getting unexpected failures with my tool w4mclassfilter (and known-good input data) and wondering whether UseGalaxy.eu is having an issue.
    "This dataset is stored in a Galaxy object store with id files10." every time.
    Arthur Eschenlauer
    @eschen42
    oh, I guess that's the object store ID, not the dataset ID. So that doesn't look like the problem.
    Gianmauro Cuccuru
    @gmauro
    We are re-deploying. Try again in a few minutes
    bgruening
    @bgruening:matrix.org
    [m]
    @jmshng_twitter: I don't think so. Both packages does not seem to be maintained :(
    Brad Langhorst
    @bwlang
    I’ve been hearing from people who are new to sequencing that they are not sure how to get started with analysis of their ARTIC data. When I recommend galaxy to these folks they are still not sure how to proceed and would like something even easier. I’m thinking about putting together a quick demonstration video about how to do it for a set of libraries. I didn’t find other resources for this via GTN, but I thought I’d just check to be sure that this is not already done or inprogress. I’d be happy to collaborate if others are working on this too.
    Dannon
    @dannon
    You're probably aware of this but the only thing I know about in Galaxy for this is https://covid19.galaxyproject.org/artic/
    bgruening
    @bgruening:matrix.org
    [m]
    @bwlangARTIC covid data?
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    heya @bwlang ! we've been discussing this a bit in galaxyproject/Public-Health - the workflow @wm75 did is the one linked in the page you mentioned. It has been used a lot in production.
    videos & a tutorial are definitely needed. let me know if you'd like a collaborator, I'd like to get something done to offer at GCC this year.
    as to the ins and outs of the workflow - these are being actively discussed in quite a few places
    Brad Langhorst
    @bwlang
    I was not aware of the Public-Health channel - good to know. I’ll probably move quickly but am happy to share whatever I come up with!
    @bgruening: yes covid data
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    Uha, then we should really also polish and update that page a bit.
    But awesome @bwlang !
    Brad Langhorst
    @bwlang
    i think it’s pretty good already! - i’d just like to see usegalaxy.org added since it’s working nicely there too. Awesome job on these workflows so far!
    bgruening
    @bgruening:matrix.org
    [m]
    I would love to see GTN videos for that!
    Will sent you 🍻 if you do that :-)
    pvanheusden
    @pvanheusden:matrix.org
    [m]
    when's next papercuts? not sure where, but issues should be filed...
    the Public Health group is new and will become louder soon
    btw as PHA4GE (https://pha4ge.org) we're collecting a list of "starting off in SARS-CoV-2 links"... I'll poke people to make it more public so that you can link to it