User: Ellie

gravatar for Ellie
Ellie20
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

<prev • 13 results • page 1 of 2 • next >
0
votes
3
answers
967
views
3
answers
Comment: C: Sequence Bias Bismark Output Interpretation
... Hi, We meet the same problem. Did you solve yours? Thank you! ...
written 12 months ago by Ellie20
0
votes
1
answer
889
views
1
answers
Comment: C: sc-WBGS library GC content, low bismark mapping rate, high CHH%
... 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 Ellie20
1
vote
1
answer
889
views
1
answer
sc-WBGS library GC content, low bismark mapping rate, high CHH%
... 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 ...
gc content methylation wgbs written 14 months ago by Ellie20 • updated 13 months ago by Felix Krueger20
0
votes
0
answers
488
views
0
answers
extremely small value on cuffnorm fpkm table
... 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 ...
fpkm cufflinks normalized value rna-seq written 2.9 years ago by Ellie20
0
votes
2
answers
2.8k
views
2
answers
Comment: C: Running Cuffmerge error "duplicate/invalid 'transcript' "
... 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 Ellie20
0
votes
4
answers
4.8k
views
4
answers
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 Ellie20
0
votes
0
answers
1.7k
views
0
answers
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 Ellie20
1
vote
2
answers
2.8k
views
2
answers
Running Cuffmerge error "duplicate/invalid 'transcript' "
... 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 ...
software error rna-seq written 3.1 years ago by Ellie20 • updated 3.0 years ago by alienbeatle.pq0
0
votes
0
answers
739
views
0
answers
multiple mapping using tophat2
... 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 ...
rna-seq written 3.1 years ago by Ellie20
0
votes
1
answer
1.6k
views
1
answers
Comment: C: cutadapt cannot work on my fastq files
... Thanks a lot! Now fastq files are right:) ...
written 3.1 years ago by Ellie20

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' "

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 649 users visited in the last hour