User: binibe

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binibe70
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Posts by binibe

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Unable to connect to galaxy FTP Server
... Hi Jen (and Shruti), I am experiencing problems with the FTP connection as well (I am using the ClassicFTP client). When logging on to usegalaxy.org with my username and password I experience no issues. But when I try to connect with the FTP client with the same username and password, I get foll ...
written 6 months ago by binibe70
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Answer: A: How to see how far in the queue a job is?
... Hi again, The Trinity-jobs I submitted Friday March 3rd and Saturday March 4th is still "waiting to run" - and I think there might be something wrong with the server/software? Are others also experiencing these long queues with Trinity (the beta version on usegalaxy.org)? Thanks, Birgitte ...
written 11 months ago by binibe70
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How to see how far in the queue a job is?
... Hi all, I have had two Trinity-jobs waiting in queue since Friday/Saturday - is there some way to see how far in the queue a job is on usegalaxy.org? Thank you! Cheers, Birgitte ...
galaxy rna-seq written 11 months ago by binibe70
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Comment: C: Fatal error in Trimmomatic
... Thank you! Don't know if this will help locate the error, but I just did a Headcrop with Trimmomatic on the data, and it worked like a charm. I then tried the IlluminaClip (Truseq3, additional) again - and the error came up again. The issue might be with the adapter trimming in some way. ...
written 11 months ago by binibe70
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Answer: A: Fatal error in Trimmomatic
... Thank you, Jennifer! I trimmed the same data (with a different Phred score) Friday morning before the error occurred and it worked fine. The files are completely loaded and in fastqsanger format. The bug was reported earlier this morning (from usegalaxy.org) since it continued to show the error. ...
written 11 months ago by binibe70
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Fatal error in Trimmomatic
... Hi all, I have been trying to run a Trimmomatic trim on my data since Friday. Trimmomatic will be running for a few seconds up to an hour before terminating with following error: > Fatal error: Exit code 1 - Trimmomatic did not finish successfully Have others experienced the same issue - or is ...
trimmomatic rna-seq written 11 months ago by binibe70
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Trimmomatic and adapters
... Hi all, As relatively new within the bioinformatics world, I am a bit confused when it comes to adapter trimming - and want to get a better understanding. At the moment I am working with PE reads generated on a NextSeq 500 - and I want to use Trimmomatic to remove adapter sequences and low quality ...
trimmomatic galaxy rna-seq written 12 months ago by binibe70
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Where can I find the Trinity statistics?
... Hi, This is maybe a stupid question, but I am new to RNA sequencing and the Galaxy environment - so I hope some experienced users can help me out. I just performed a Trinity assembly (from PE reads data) - and now I want to see the statistics on the assembly (# contigs, N50 etc.). It was my impr ...
rna-seq trinity assembly written 13 months ago by binibe70 • updated 12 months ago by raggieapauly0
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Answer: A: allocated quota? Why?
... Hi :) Try this: Go to: "Saved histories" --> "Advanced search" --> set "status" to all --> then you can permanently delete the data and free some space :-) ...
written 13 months ago by binibe70
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Comment: C: Disk quota issue
... Thank you, Jen! I am now down to 31% of disk space used :-) ...
written 13 months ago by binibe70

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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: allocated quota? Why?

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