User: simplitia

gravatar for simplitia
simplitia40
Reputation:
40
Status:
New User
Location:
Last seen:
1 month ago
Joined:
4 years, 11 months ago
Email:
s********@gmail.com

Posts by simplitia

<prev • 34 results • page 1 of 4 • next >
1
vote
0
answers
152
views
0
answers
Convert COSMIC VCF coordinates to that of ensembl format?
... HI so I downloaded the mutation VCF from COSMIC recently and realized that the coordinates are ones without the "chr" prefix so I'm wondering there are any tools to convert this coodinate sys to one without the chr prefix ( I believe this is the ensemble one). I can use awk to replace and add +1, ...
alignment next-gen snp sequencing written 4 months ago by simplitia40
0
votes
2
answers
1.9k
views
2
answers
Answer: A: Checking integrity of SRA downloaded fastq files
... I ran into the same issue in that the vdb-validate does not work if you are downloading the fastq files without prefetching the sra, you are left with only a fastq file which cannot be validated. It strange that the there isn't a simple checksum that is provided, may be we can get the admin to incl ...
written 6 months ago by simplitia40
0
votes
0
answers
231
views
0
answers
Where can I get the GTex equivalent to rnaseqv2 Level3 RSEM_genes?
... Hi I want to compare TCGA lung cancer to normal lung in GTex. Currently I download expected_counts/raw counts from Gdac firehouse. My understanding is that this is from the Tcga Rnaseqv2 Level3 Data pipeline. However Gdac does not have GTex data. My question, do you know where I can download GT ...
tcga rna-seq rsem written 7 months ago by simplitia40
0
votes
6
answers
21k
views
6
answers
Comment: C: How To Do Normalization Of Two Chip-Seq Data?
... Would one have to first normalize to total reads? For example in one of the GEO set I downloaded recently the one sample had 65 million spot # whilst the other had 63 million. In this case is it necessary to first scale by total counts first? Thanks! ...
written 9 months ago by simplitia40
0
votes
1
answer
735
views
1
answers
Comment: C: How to round the "expected counts" to integers?
... Hi others might have other opinion but I think you can just simply round the numbers to nearest integer, this should be good enough. tximport power is to utilize the bootstrapping form things like kalliso but you don't have it here thus I don't think it be that much more useful but I could be wrong ...
written 9 months ago by simplitia40
1
vote
3
answers
320
views
3
answers
How reliable are the ensembl transcript isoforms?
... Hi, I was reading a recent article that mentions that there were two isoform for a particular gene they were interests in. However when I went to ensembl it turns out that there were a lot more including non protein versions. The question is I'm assuming in the ensembl transripts they are all pred ...
ensembl rna-seq isoform written 11 months ago by simplitia40 • updated 10 months ago by Astrid_Ensembl330
2
votes
1
answer
500
views
1
answer
GRanges: remove ranges that falls in between a larger range?
... Hi suppose I have a grange object as such, g <- GRanges(seqnames=c(rep("Chr1",3)), strand=rep("+",3), ranges=IRanges(start=c(10,2,2), end=c(24,27,30))) this produces a grange that looks like this. GRanges object with 3 ranges and 0 metadata columns: seqnames ranges stran ...
R grange rna-seq written 11 months ago by simplitia40 • updated 11 months ago by Strand NGS40
0
votes
2
answers
5.1k
views
2
answers
Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
... Ok this great however does anyone know how to assign a color say grey to a node with no value ( NA ) the issue I have is the value is not availaible cytoscape will just color it with the maximum color! ...
written 13 months ago by simplitia40
0
votes
2
answers
7.7k
views
2
answers
Answer: A: TMM or TPM normalized counts for visualization?
... To add to this, why not both. You can also get tpmTMM normalized- the benefit of this is to stabilize rna composition. ...
written 16 months ago by simplitia40
1
vote
1
answer
752
views
1
answer
STAR: Is it ok to align with an index created from genecode but count features from gtf from ensembl?
... I'm wondering if there maybe some coordinate issues as with UCSC and ensembl. I happen to have bam files which were aligned with STAR using indices that were created from gencode however, I would like to use htseq count but with gtf donwloaded from ensembl instead? thanks! A ...
alignment star rna-seq written 17 months ago by simplitia40 • updated 17 months ago by kristoffer.vittingseerup3.5k

Latest awards to simplitia

Popular Question 10 months ago, created a question with more than 1,000 views. For How to quantify PCR duplication from bam file
Popular Question 12 months ago, created a question with more than 1,000 views. For Help with BWA: how to align paired as single and then combine again
Popular Question 16 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 17 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 20 months ago, created a question with more than 1,000 views. For Create fusion transcripts with breakpoint coordinates from two genes.
Popular Question 20 months ago, created a question with more than 1,000 views. For Hard time trying to calculate Allele Frequency and DP from Platypus

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1579 users visited in the last hour
_