User: keren.maor

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keren.maor40
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Posts by keren.maor

<prev • 11 results • page 1 of 2 • next >
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hierarchical clustering heat map in Galaxy
... Hi all, I'm looking for a tool that can produce a hierarchical clustering heat map in Galaxy for RNAseq data (with TPM values for instance). Is anyone familiar with something like that in Galaxy? I have not found anything so far. Thank you ...
clustering heat map galaxy rna-seq written 24 days ago by keren.maor40
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visualization tutorial galaxy
... Hi all, I'm looking for visualization tools in Galaxy for presenting RNAseq results, such as generating: Venn diagram, heat map, PCA, etc. Is anyone aware of a good tutorial describing what are the options for these in Galaxy? Thank you ...
galaxy visualization figures rna-seq written 9 weeks ago by keren.maor40 • updated 8 weeks ago by Martin Čech ♦♦ 4.8k
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Comment: C: Duplicate seq ids in uniref50
... I tried to use the tool NormalizeFasta (basically cut down the uniref annotation and left with only the id code), and than to Makeblastdb, but again I got the error message :"30757757 sequences Fatal error: Exit code 1 () BLAST Database creation error: Error: Duplicate seq_ids are found: GNL|BL_ORD ...
written 9 weeks ago by keren.maor40
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Answer: A: Duplicate seq ids in uniref50
... Thank you Jen for your reply. I will try it as well. did you mean to turn the option :"Truncate sequence names at first whitespace" to Yes? ...
written 9 weeks ago by keren.maor40
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salmon output files in Galaxy
... Hi all, I used Salmon tool in Galaxy to both align to my de novo transcriptome assembly and to quantify number of reads per transcript (assembled using Trinity--> Transdecoder). I got two output files per sample, named :" Quantification" and "Gene quantification". I don't understand what is the d ...
quantification galaxy salmon rna-seq written 9 weeks ago by keren.maor40 • updated 8 weeks ago by Jennifer Hillman Jackson25k
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Duplicate seq ids in uniref50
... Dear all, I was trying to generate a protein database using the Galaxy tool NCBI BLAST+ makeblastdb, with a fasta file of Uniref50 (downloaded here: http://www.uniprot.org/downloads). This is so I could do blastP to my Transdecoder output of de novo transcriptome assembly. I received an error messag ...
galaxy blast uniref50 rna-seq written 9 weeks ago by keren.maor40
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error running BUSCO in Galaxy
... Dear all, I'm trying to run BUSCO via Galaxy (Melbourne server) to asses my de novo assembled transcriptome, but keep getting error message :" An error occurred with this dataset: /mnt/galaxy/tmp/job_working_directory/000/100/100295/tool_script.sh: line 9: run_BUSCO.py: command not found". Does anyo ...
de novo rna-seq galaxy busco assembly written 10 weeks ago by keren.maor40 • updated 8 weeks ago by Jennifer Hillman Jackson25k
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Comment: C: problems with installing a tool from Galaxy tool shed
... Thank you for your reply. I was not aware that I need to be an administrator for installing tools. I will try to update to admin account. ...
written 3 months ago by keren.maor40
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problems with installing a tool from Galaxy tool shed
... Hi, I'm trying to install Trinity from the Galaxy tool shed and have been getting this error. "Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable third-party cookies in your browser." I have checked my browser for allowing third-party cookies, and tr ...
galaxy install admin tool written 3 months ago by keren.maor40 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: Installing a Tool from Tool shed in Browser ~ Third Party Cookies
... I'm also trying to install Trinity from the Galaxy tool shed and have been getting this error. I tried chrome, internet explorer and firefox, all with allowing third-party cookies. Does anyone know how to solve this? thank you ...
written 3 months ago by keren.maor40

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