User: I0110
I0110 • 90
- Reputation:
- 90
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- United States
- Last seen:
- 5 days, 3 hours ago
- Joined:
- 2 years, 5 months ago
- Email:
- h****@ncsu.edu
Posts by I0110
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... 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
I0110 • 90
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... 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 ...
written 7 weeks ago by
I0110 • 90
• updated
7 weeks ago by
rajeev.vikram • 20
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... 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 ...
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... I really did not know that normalization could be done before log2-transformation. Thanks for sharing the knowledge, Ahill. ...
written 3 months ago by
I0110 • 90
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... 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! ...
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... 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
I0110 • 90
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... 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
I0110 • 90
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... 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 ...
written 3 months ago by
I0110 • 90
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... 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 ...
written 7 months ago by
I0110 • 90
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Comment:
C: Host bam file on MongoDB?
... If I have a mlab account, can I consider that my server? ...
written 8 months ago by
I0110 • 90
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