User: Widmer, Giovanni

Reputation:
150
Status:
Trusted
Location:
US, Tufts University
Last seen:
3 months, 1 week ago
Joined:
7 years, 6 months ago
Email:
g**************@tufts.edu

Posts by Widmer, Giovanni

<prev • 11 results • page 1 of 2 • next >
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News: thank you galaxy team
... On the eve before Thanksgiving, a special THANK YOU to the galaxy team and to Jen for providing such a fine resource and answering our many queries so promptly. To all of the members of the galaxy community, if you celebrate Thanksgiving, my best wishes for a wonderful day. Giovanni Widmer ...
news galaxy written 11 months ago by Widmer, Giovanni150
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Answer: A: HiSAT2 Alignment Rate Dropping with Cufflinks export option enabled
... Hi, similar observation here. I align 100-nt single-end RNA-Seq reads to the built-in Sus scofa genome. I have 7,000,000 reads per sample. I get in the vicinity of 50% aligned sequences. What puzzles me is that if I BLAST randomly selected unaligned reads into genbank they all perfectly align to pig ...
written 12 months ago by Widmer, Giovanni150
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Comment: C: Error message in Tophat
... Hi, I get same same error message in TopHat: "An error occurred setting the metadata for this dataset". Cufflinks stays on gray with "!" icon. I deleted Cufflinks, purged deleted and refreshed history. Re-ran cufflinks and same problem. Re-setting metadata generates this message: "Attributes updated ...
written 23 months ago by Widmer, Giovanni150
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Thank you galaxy team!
... In the spirit of Thanksgiving, I would like to say Thank You to Jen and the galaxy team for providing high-quality and prompt support. It makes all the difference for us here in the trenches! Giovanni ...
galaxy written 23 months ago by Widmer, Giovanni150 • updated 23 months ago by Bjoern Gruening5.1k
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Answer: A: Cufflinks returns 0 FPKM
... Hi Jen, thanks for the quick response. After re-running Cufflinks in usegalaxy.org with the built-in susScr3 ref genome and the annotation file from iGenomes, I don't see any gene IDs in the cufflinks gene expression output file. Instead I see cuff.1, cuff.2 etc. under tracking ID and gene ID. Shoud ...
written 23 months ago by Widmer, Giovanni150
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Cufflinks returns 0 FPKM
... Hi, I realize that many users have posted similar questions and the galaxy team has diligently addressed dozens of similar queries. After reading whatever I could find on the subject, I am still in the dark on how to fix my annotation file, assuming that's what causes cufflinks to return FPKM of zer ...
cufflinks rna-seq written 23 months ago by Widmer, Giovanni150
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Answer: A: Error executing tool: maximum recursion depth exceeded while calling a Python ob
... thanks Jen. I use a local galaxy at http://galaxy.med.tufts.edu/. I re-loaded the genome FASTA file and ran TopHat again and now I get another error: Error in tophat: [Fri Nov 4 13:10:25 2016] Beginning TopHat run (v1.4.1) ----------------------------------------------- [Fri Nov 4 13:10:25 2016] ...
written 23 months ago by Widmer, Giovanni150
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Error executing tool: maximum recursion depth exceeded while calling a Python object
... Hi, I'm using a custom genome (in FASTA format) which I downloaded from EupathDB.org. I used User/Custom builds and edited the attributes per galaxy instructions. When I run tophat I get the following error message: Error executing tool: maximum recursion depth exceeded while calling a Python objec ...
custom-genome tophat error written 23 months ago by Widmer, Giovanni150 • updated 23 months ago by Jennifer Hillman Jackson25k
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Answer: A: merging two unrelated reference genomes and annotation files
... thanks for your help, Jen. Which Concatenate tool do I use to merge 2 genome fasta files? Concatenate Fasta Alignment by Species (under Fasta Manipulation) seems to be the only tool that requires a FASTA formatted input file. For merging two GTF annotation files, do I use Concatenate datasets tail-t ...
written 24 months ago by Widmer, Giovanni150
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merging two unrelated reference genomes and annotation files
... Hi, I work with an intracellular pathogen. I would like to run an RNA-Seq analysis in galaxy using a combined host-parasite transcriptome as reference and annotation (gtf) file. I expect about 2% of my reads are of pathogen origin and the remaining 98% of host origin. How do I create a combined host ...
custom-genome cufflinks tophat rna-seq written 24 months ago by Widmer, Giovanni150

Latest awards to Widmer, Giovanni

Popular Question 10 months ago, created a question with more than 1,000 views. For merging two unrelated reference genomes and annotation files
Appreciated 23 months ago, created a post with more than 5 votes. For Thank you galaxy team!
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For Thank you galaxy team!
Student 23 months ago, asked a question with at least 3 up-votes. For Thank you galaxy team!

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