User: aditi.qamra

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aditi.qamra260
Reputation:
260
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Trusted
Location:
Toronto
Twitter:
itti_q
Scholar ID:
Google Scholar Page
Last seen:
3 weeks ago
Joined:
5 years, 7 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 • 64 results • page 1 of 7 • next >
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Answer: A: how to merge different peak sparse matrices
... hey - you can't directly merge these matrices since the peaks are not exactly the same. 1) make a consensus peakset from the peak files called by 10x 2) get readcounts in the consensus peakset from all cells of all your samples -- that would be your final matrix of interest ...
written 4 weeks ago by aditi.qamra260
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Comment: C: ballgown has "." as Gene Names
... Can you post your code here? ...
written 9 weeks ago by aditi.qamra260
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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 10 weeks ago by aditi.qamra260
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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 10 weeks ago by aditi.qamra260
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Comment: C: Protist in UniProt/NCBI taxonomic tree
... Try - http://protists.ensembl.org/info/website/ftp/index.html ...
written 10 weeks ago by aditi.qamra260
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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 10 weeks ago by aditi.qamra260
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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 8 months ago by aditi.qamra260
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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 8 months ago by aditi.qamra260
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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 8 months ago by aditi.qamra260 • updated 8 months ago by bioExplorer3.7k
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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 17 months ago by aditi.qamra260

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Popular Question 11 months ago, created a question with more than 1,000 views. For Transcript support level in Gencode gtf v19
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Popular Question 23 months ago, created a question with more than 1,000 views. For Calculate complete Splicing Index (coSI) for exons
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Average Width Of H3K4Me3 Peaks
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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Combined Tss Plots For Chip Seq Peaks
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