User: newbie
newbie • 70
- Reputation:
- 70
- Status:
- Trusted
- Location:
- Last seen:
- 1 week, 4 days ago
- Joined:
- 1 year, 1 month ago
- Email:
- m******************@gmail.com
Posts by newbie
<prev
• 49 results •
page 1 of 5 •
next >
0
votes
1
answer
132
views
1
answers
... thanq. And I posted may doubt in support bioconductor also. I got the reply. Here it is https://support.bioconductor.org/p/129140/#129223 ...
written 14 days ago by
newbie • 70
0
votes
1
answer
132
views
1
answers
... I found an R package [GenomicScores][1] to extract the `phastcons` scores.
In the tutorial of the `GenomicScore` I see that information can be exxtracted only by each chromosome location.
But I would like to know, whether there is any way to get the `phastcons` score for all protein coding genes ...
written 16 days ago by
newbie • 70
0
votes
1
answer
132
views
1
answers
... For the newly found lncRNAs, yes I will do it myself using `phast`. But how do I get the `phastcons` score for gencode protein-coding genes and known lncRNAs? ...
written 17 days ago by
newbie • 70
2
votes
1
answer
132
views
1
answer
...
Dear All,
I'm interested in checking the conservation of lncRNAs and protein-coding genes from Gencode and similarly from my data I also have some newly assembled lncRNAs which are not found in gencode. I would like to make a plot like below:
![enter image description here][1]
The above image is ...
0
votes
1
answer
80
views
1
answers
... thanks a lot for the reply and the clear explanation. So, if the p-value is less than 0.05 it is seen as they are mutually exclusive. Am I right? ...
written 26 days ago by
newbie • 70
3
votes
1
answer
80
views
1
answer
...
I have a total of 4500 samples. Among them `GeneA` is mutated in 600 and `GeneB` is in 900.
Mutations in both `GeneA` and `GeneB` are 90
Mutations in only `GeneA` and no mutation in `GeneB` are 550
Mutations in only `GeneB` and no mutation in `GeneA` are 810
I see some people use fishers test t ...
0
votes
3
answers
263
views
3
answers
... small question. I have the sorted.bam files from `Hisat2` alignment. Can I use those bams for `RSEM` to calculate transcript expression? ...
written 5 weeks ago by
newbie • 70
0
votes
3
answers
263
views
3
answers
... you mean I can't get transcript level read counts with featureCounts? ...
written 5 weeks ago by
newbie • 70
16
votes
3
answers
263
views
9 follow
3
answers
... I have used `featureCounts` to get the read counts one a gene level with the following command:
featureCounts -a gencode.gtf -F GTF -p -s 2 -T 8 -o sample.txt sample.sorted.bam
I'm interested in extracting the counts on a transcript level. My data is paired end and reverse stranded. I'm a bit ...
written 5 weeks ago by
newbie • 70
• updated
5 weeks ago by
Gordon Smyth • 1.5k
0
votes
1
answer
126
views
1
answers
... thanks a lot @ATpoint ...
written 5 weeks ago by
newbie • 70
Latest awards to newbie
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 912 users visited in the last hour