Dataset Not Appearing As Available Input To Sam Analyses

Question: Dataset Not Appearing As Available Input To Sam Analyses

7.1 years ago by

Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown. Thanks Clare Nelson

• 857 views

ADD COMMENT • link •

modified 7.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.1 years ago by James Nelson • 10

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Clare, Perhaps the loaded pileup datasets are not assigned to the "pileup" datatype? Click on the pencil icon in the right upper corner of the loaded pileup dataset, then use "Edit Attributes -> Change data type". Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

7.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Clare, Galaxy is fairly transparent, so this occurs sometimes and can mean that either the server is very busy or there is another problem, perhaps with the dataset. Please note that mpileup is not supported yet, just pileup, although this is on our short list of to-do upgrades. If you used mpileup, this could very likely be the root cause of the tool error ("server error"). You can track the upgrade to mpileup through this ticket: https://bitbucket.org/galaxy/galaxy-central/issue/524 To troubleshoot a pileup file: 1 - double check the format of your data again the specification as outlined on the tool form for "NGS: SAM Tools -> Generate pileup from BAM dataset". 2 - try running the file type assignment again the job again to double check against a transient error. If pileup was used and the cause of the error is still unclear, we take a look we can provide feedback. Please share a link to your history using "Options -> Share or Publish" from the top of the history panel, generate a share link, then email that back to me directly. Please note which dataset presents the problem and confirm that "samtools pileup" was used. Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 7.1 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »