User: aditi.qamra

gravatar for aditi.qamra
aditi.qamra250
Reputation:
250
Status:
Trusted
Location:
Toronto
Twitter:
itti_q
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
5 years, 5 months ago
Email:
a**********@gmail.com

Postdoc at Princess Margaret Cancer Center, Toronto. Ph.D. from Genome Institute of Singapore.

Posts by aditi.qamra

<prev • 63 results • page 1 of 7 • next >
0
votes
1
answer
55
views
1
answers
Comment: C: ballgown has "." as Gene Names
... Can you post your code here? ...
written 2 days ago by aditi.qamra250
0
votes
1
answer
48
views
1
answers
Answer: A: Do some cancer type data in RTCGA cannot be downloaded?
... Seems like ACC.mRNA is not included in the RTCGA.mRNA package. You can use Xena browser (https://xenabrowser.net/) or http://firebrowse.org/ to download gene expression for ACC. ...
written 8 days ago by aditi.qamra250
0
votes
1
answer
61
views
1
answers
Answer: A: compute genome composition (total amount of introns/exons etc)
... You can parse the TxDb object you used for this genome to annotate the peaks in the first place. See http://genomicsclass.github.io/book/pages/bioc1_annoOverview.html ...
written 8 days ago by aditi.qamra250
1
vote
0
answers
95
views
0
answers
Comment: C: Protist in UniProt/NCBI taxonomic tree
... Try - http://protists.ensembl.org/info/website/ftp/index.html ...
written 8 days ago by aditi.qamra250
1
vote
1
answer
55
views
1
answers
Answer: A: ballgown has "." as Gene Names
... Did you do a denovo assembly ? If so, you will have to first add the gene names by using getGenes() and a gtf file. Also check what is the output of indexes(ballgown_obj1)$t2g ...
written 8 days ago by aditi.qamra250
0
votes
1
answer
334
views
1
answers
Comment: C: Mismatch number of reads after bedtools bam2fastq on RNA-seq data
... Thanks h.mon. I did sort them before using bedtools. But you are right it is because of multimappers in the bam. ...
written 6 months ago by aditi.qamra250
0
votes
1
answer
334
views
1
answers
Comment: C: Mismatch number of reads after bedtools bam2fastq on RNA-seq data
... Thanks Vijay! Sorry I dint know about this option before. Will take care ...
written 6 months ago by aditi.qamra250
1
vote
1
answer
334
views
1
answer
Mismatch number of reads after bedtools bam2fastq on RNA-seq data
... Hi, I am trying to generate fastqs ( to realign them with different parameters) from RNA-seq bams aligned using STAR (run with --outSAMunmapped Within flag). The original fastq was paired end and stranded and I don't have access to that. I used bedtools bam2fastq ( `bedtools bamtofastq -i $bam -fq ...
alignment rna-seq written 6 months ago by aditi.qamra250 • updated 6 months ago by Vijay Lakhujani3.5k
1
vote
0
answers
595
views
0
answers
Comment: C: Explain fig. 5 c of "The impact of rare variation on gene expression across tiss
... Here's my quick attempt - Again from the biorxiv version - Although RIVER was trained in an unsupervised manner, **the learned model prioritized variants that were supported by both extreme expression levels for a nearby gene and genomic annotations suggestive of potential impact (Fig.5c)**. Rather ...
written 15 months ago by aditi.qamra250
1
vote
0
answers
595
views
0
answers
Comment: C: Explain fig. 5 c of "The impact of rare variation on gene expression across tiss
... I am still trying to understand but the biorxiv version has a better legend for the same figure - "Distribution of RIVER scores (shades of blue) as a function of scores from genomic annotation or gene expression alone. Pathogenic SNVs annotated in ClinVar are shown in red if they were likely regulat ...
written 15 months ago by aditi.qamra250

Latest awards to aditi.qamra

Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.
Popular Question 9 months ago, created a question with more than 1,000 views. For Transcript support level in Gencode gtf v19
Popular Question 10 months ago, created a question with more than 1,000 views. For Transcript support level in Gencode gtf v19
Popular Question 13 months ago, created a question with more than 1,000 views. For Transcript support level in Gencode gtf v19
Popular Question 17 months ago, created a question with more than 1,000 views. For Transcript support level in Gencode gtf v19
Popular Question 21 months ago, created a question with more than 1,000 views. For Calculate complete Splicing Index (coSI) for exons
Popular Question 23 months ago, created a question with more than 1,000 views. For Chromosomal Information For Gene List In Microarray Data
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Average Width Of H3K4Me3 Peaks
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Covariate Selection For Microarray Data
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Average Width Of H3K4Me3 Peaks
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Average Width Of H3K4Me3 Peaks
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Combined Tss Plots For Chip Seq Peaks
Popular Question 3.3 years ago, created a question with more than 1,000 views. For GSEA Error Message - "Dataset not set"
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Combined Tss Plots For Chip Seq Peaks
Voter 4.1 years ago, voted more than 100 times.
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: GC content of promoters
Supporter 4.7 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1291 users visited in the last hour