User: Ellie
Ellie • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- United States
- Last seen:
- 11 months, 1 week ago
- Joined:
- 3 years, 2 months ago
- Email:
- j***********@uconn.edu
Posts by Ellie
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0
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... Hi, We meet the same problem. Did you solve yours?
Thank you! ...
written 12 months ago by
Ellie • 20
0
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1
answer
889
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1
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... Hi, Felix,
Thank you very much for your reply.
I tried single-mode to align in Bismark, the mapping rate does not increase too much, only 1-3%. I also tried L,0,-0.4, the mapping rate in one library dropped from 10.6% to 7.6%, but the non-CG methylation only dropped from 7% to 6% still is ...
written 12 months ago by
Ellie • 20
1
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1
answer
889
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1
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... Hi, I have met some problem in analysis sc-WGBS dataset. The single cell WGBS experimental protocol was followed the nature protocol: [Smallwood et.al][1]. This is in Bovine, we used the genome [UMD3.1.1][2]
This is the fast-QC GC-content before TrimGalore
After the first 12bp were trimmed off ...
written 14 months ago by
Ellie • 20
• updated
13 months ago by
Felix Krueger • 20
0
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0
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488
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... Hi, all,
I got some weird values in genes.fpkm_table after cuffnorm. They are really small like "2.88416e-271", "8.78893e-260" "8.89433e-194", there are many in my data, so I'm wondering is this normal to get for fpkm? Any idea what's wrong?
Thanks for the help!
Best,
Ellie
...
written 2.9 years ago by
Ellie • 20
0
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2
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2.8k
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2
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... Hi, Kanne,
Thanks a lot for your reply, yes exactly, I tried all kinds of ways, but seems like every round of cufflinks (I was using -G newest bovine genome UMD3.1.1 ) will generate some multiple transcripts id duplicates (they share the same transcripts id but exons all marked as "exon1", co ...
written 3.0 years ago by
Ellie • 20
0
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4
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4.8k
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4
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Comment:
C: Cuffmerge running error
... Hi, Hana,
How did you solve your problem? I got exact same one. Really need your suggestion.
Thanks!
Best,
Ellie
...
written 3.1 years ago by
Ellie • 20
0
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0
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1.7k
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0
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Comment:
C: Ensembl Gtf Cuffmerge Duplicates
... Hi Andrew,
I am running cuffmerge using cufflinks v2.1.1 and I ran into the exact same problem you mentioned above. I was wondering if you ever figured it out?
Thanks,
Ellie
...
written 3.1 years ago by
Ellie • 20
1
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2
answers
2.8k
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2
answers
... Hi, all,
I use cuffmerge after tophat2 & cufflinks for all the transcripts.gtf files, there is an issue shows up:
" [12:50:00] Loading reference annotation.
GFF Error: duplicate/invalid 'transcript' feature ID=id234068
[FAILED]
Error: could not execute gtf_to_sam "
I found t ...
written 3.1 years ago by
Ellie • 20
• updated
3.0 years ago by
alienbeatle.pq • 0
0
votes
0
answers
739
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0
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... Hi,
I want to include the gene paralogs by using tophat2 "non-uniquely mapping" to allow multiple reads aligned to the reference genome. I used default -k =1, and -m = int, will this make non-uniquely mapping achieved?
First time doing the mapping, thanks a lot for the help!
Best,
Ellie
...
written 3.1 years ago by
Ellie • 20
0
votes
1
answer
1.6k
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1
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... Thanks a lot! Now fastq files are right:)
...
written 3.1 years ago by
Ellie • 20
Latest awards to Ellie
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
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