User: Biodata_ed
Biodata_ed • 20
- Reputation:
- 20
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- Location:
- United States
- Last seen:
- 1 day, 21 hours ago
- Joined:
- 3 years, 11 months ago
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- j***********@uconn.edu
Posts by Biodata_ed
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... I'm having similar mapping results to dm6 too, some sample is lower than 5% and some is higher than 70%. Did you solve your mapping problem? Any suggestions? Thank you! ...
written 8 weeks ago by
Biodata_ed • 20
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... Hi, We meet the same problem. Did you solve yours?
Thank you! ...
written 21 months ago by
Biodata_ed • 20
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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 21 months ago by
Biodata_ed • 20
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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 22 months ago by
Biodata_ed • 20
• updated
22 months ago by
Felix Krueger • 40
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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 3.7 years ago by
Biodata_ed • 20
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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 3.7 years ago by
Biodata_ed • 20
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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 3.8 years ago by
Biodata_ed • 20
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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 3.8 years ago by
Biodata_ed • 20
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... 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 3.8 years ago by
Biodata_ed • 20
• updated
3.7 years ago by
alienbeatle.pq • 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 3.9 years ago by
Biodata_ed • 20
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20 months ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
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23 months ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
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2.9 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Running Cuffmerge error "duplicate/invalid 'transcript' "
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