User: Rituriya

gravatar for Rituriya
Rituriya20
Reputation:
20
Status:
New User
Location:
Canada
Last seen:
4 weeks ago
Joined:
7 years, 5 months ago
Email:
p***********@gmail.com

I am a Bioinformatician since 2009, working on various types of Next generation sequencing datasets. Mostly using open source tools and softwares to analyze the data. Keen on understanding how machine learning and AI go hand in hand and would love to learn more programming in my free time.  

Posts by Rituriya

<prev • 28 results • page 1 of 3 • next >
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Finding a biomarker from DE genes
... Hi All, I have around say 150 differentially expressed (DE) genes between 2 groups (control and treatment of a disease) by RNA-seq. My goal is to really shorten this list and find that few number of genes, which are of utmost significance which acts as a marker for this disease. Now my problem is ...
mirna biomarker differential expression rna-seq written 9 weeks ago by Rituriya20 • updated 9 weeks ago by Buffo1.6k
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Comment: C: miRNA analysis by miRDeep2
... Hi Xin, I am also perplexed as to how to find common set of miRNAs across samples and their expression levels. Also, there is no direct list generated, which gives the user a common set of novel miRNAs across samples, as they have randomly generated IDs. If you get an answer, please post it here fo ...
written 5 months ago by Rituriya20
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Comment: C: miRPara for novel miRNA discovery
... Sure, I will give it a try. Thank you. ...
written 5 months ago by Rituriya20
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miRPara for novel miRNA discovery
... Has anyone used the tool named '[miRPara][1]' for novel discovery of miRNAs? It seems to be quite an old tool (last update 2013). After a cumbersome installation of the tool, I am always getting zero miRNAs as output. I am a novice when it comes to dealing with novel miRNA discovery. I have tried ...
mirpara novel mirna written 5 months ago by Rituriya20 • updated 5 months ago by v82masae140
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Comment: C: De-duplicate UMI at FASTQ level
... Interesting. Thank you Ian. ...
written 5 months ago by Rituriya20
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Comment: C: De-duplicate UMI at FASTQ level
... I have almost full clarity on these parameters (aligner used, settings, version of miRBase etc) just not the UMI based collapsing of reads which they do before alignment. But yes, I agree to your thoughts. ...
written 5 months ago by Rituriya20
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Comment: C: De-duplicate UMI at FASTQ level
... I wanted to keep it conservative as we have already processed this data by a commercial software and I am trying to reproduce the same results. Now the problem is they have collapsed reads before alignment and I do not see anyone else doing that. There is a huge difference in the counts for each miR ...
written 5 months ago by Rituriya20
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Comment: C: De-duplicate UMI at FASTQ level
... Absolutely. That was the first step as I mentioned earlier. Also I kept only those reads which had the adapters in them, which is approx 47% of reads. ...
written 5 months ago by Rituriya20
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Comment: C: De-duplicate UMI at FASTQ level
... So here 13% means 13% of total raw reads got aligned. If you measure from total reads of previous step (take aligned reads and map to RFAM db and retain only miRNA related reads), then it is 47.6% aligned to mature miRNA, which is not bad I feel. Right? ...
written 5 months ago by Rituriya20
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Comment: C: De-duplicate UMI at FASTQ level
... UMI length=12 bp, Raw reads around 20 million reads per sample and for the stats file, there are 3 files generated. Below is the edit_distance.tsv file: directional directional_null edit_distance unique unique_null 3193 3193 Single_UMI 2173 2173 0 75 ...
written 5 months ago by Rituriya20 • updated 5 months ago by genomax69k

Latest awards to Rituriya

Autobiographer 10 weeks ago, has more than 80 characters in the information field of the user's profile.
Great Question 2.8 years ago, created a question with more than 5,000 views. For Collapse Probes For Same Gene
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Collapse Probes For Same Gene

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