User: I0110

gravatar for I0110
I011090
Reputation:
90
Status:
Trusted
Location:
United States
Last seen:
5 days, 3 hours ago
Joined:
2 years, 5 months ago
Email:
h****@ncsu.edu

Posts by I0110

<prev • 31 results • page 1 of 4 • next >
0
votes
1
answer
207
views
1
answers
Comment: C: How to fix 5'UTR annotation with RNA-seq data?
... Yes, this has been verified in many data sets, using many different aligners. Is there a tool or method to systematically fixing this type of annotation issue (i.e. give me a new gtf with updated 5'UTR for all genes)? ...
written 7 weeks ago by I011090
0
votes
1
answer
207
views
1
answer
How to fix 5'UTR annotation with RNA-seq data?
... Hi, I am studying the transcriptome of Arabidopsis. Interestingly, the 5' UTR of the annotation is usually too long. Here is an [example][1]. You can see the RNA-seq reads covers a much smaller region of the annotated 5' UTR. Is there a way to fix that? I hope to get the gtf of the shorter isofor ...
rna-seq written 7 weeks ago by I011090 • updated 7 weeks ago by rajeev.vikram20
2
votes
1
answer
215
views
1
answer
Identify transcription start site using RNA-seq data
... I am wondering if there is a tool available to identify eukaryotic transcription start site using regular RNA-seq data? I know people use cap-seq to select 5' cap of mRNA and sequence them. However, there are a lot more RNA-seq data available. It would be interesting if we can try using RNA-seq data ...
rna-seq written 12 weeks ago by I011090 • updated 12 weeks ago by ababaian20
0
votes
1
answer
188
views
1
answers
Comment: C: The use of "and" in bioinformatics literature
... I really did not know that normalization could be done before log2-transformation. Thanks for sharing the knowledge, Ahill. ...
written 3 months ago by I011090
1
vote
1
answer
188
views
1
answer
The use of "and" in bioinformatics literature
... Sorry, this is basically an English problem. I am reading a paper which mentioned they normalized and log2 transformed their microarray data. Does that imply any relationship in time? I meant: did they normalize the data first then log2 transform the data? Thanks! ...
microarray written 3 months ago by I011090 • updated 3 months ago by Ahill1.1k
0
votes
1
answer
301
views
1
answers
Comment: C: In gff3 format, could one eukaryotic mRNA contain more than one protein coding s
... Brilliant, mbens! Indeed, "polycistronic" is exactly what I was looking for and should be used for this question. For the gene I have been working on, it is one gene/transcript by annotation, but riboseq data suggests 2 possible ORFs with different peptide sequences. By annotation, it is one gene. I ...
written 3 months ago by I011090
0
votes
1
answer
301
views
1
answers
Comment: C: In gff3 format, could one eukaryotic mRNA contain more than one protein coding s
... Hi, mbens, thanks for your help. What I meant is actually: Can one gene/mRNA contains more than one open reading frames? Not CDS. I updated the question. My apologies. ...
written 3 months ago by I011090
7
votes
1
answer
301
views
1
answer
In the gff3 format, could one eukaryotic mRNA contain more than one protein coding sequences (i.e. polycistronic)?
... Below is a simple example of gff3 file: 1 T1 gene 3631 4605 . + . ID=ATNG01010 1 T1 mRNA 3631 4605 . + . ID=ATNG01010.1;Parent=ATNG01010 1 T1 exon 3631 3913 . + . ID=ATNG01010:exon:1;Parent=ATNG01010.1 1 T1 CDS 3860 3913 . + 0 ID=ATNG01010:CDS:1;Parent=ATNG01010.1 1 T1 exon 3996 ...
gff3 annotation written 3 months ago by I011090
0
votes
0
answers
260
views
0
answers
bed file to gtf/gff
... Hi, I have a bed file with. column 1: chromosome number column 2: exon start column 3: exon stop column 4: gene name column 5: start of coding sequence (CDS) column 6: end of coding sequence (CDS) column 7: strand See below for example. Is there a way to transform it to gtf/gff for ...
genome annotation written 7 months ago by I011090
0
votes
0
answers
470
views
0
answers
Comment: C: Host bam file on MongoDB?
... If I have a mlab account, can I consider that my server? ...
written 8 months ago by I011090

Latest awards to I0110

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 669 users visited in the last hour