User: Rituriya

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Rituriya20
Reputation:
20
Status:
New User
Location:
Canada
Last seen:
5 days, 21 hours ago
Joined:
7 years ago
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p***********@gmail.com

Posts by Rituriya

<prev • 27 results • page 1 of 3 • next >
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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 11 days ago by Rituriya20
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Comment: C: miRPara for novel miRNA discovery
... Sure, I will give it a try. Thank you. ...
written 18 days 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 18 days ago by Rituriya20 • updated 18 days ago by v82masae100
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Comment: C: De-duplicate UMI at FASTQ level
... Interesting. Thank you Ian. ...
written 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks ago by Rituriya20 • updated 4 weeks ago by genomax62k
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Comment: C: De-duplicate UMI at FASTQ level
... > Adapter trimming -> UMI extraction using UMI_tools -> Align to PhiX -> > take unmapped reads -> align to genome (99.5% alignment perc)-> take > aligned reads and map to RFAM db and retain only miRNA related reads > -> align with miRBase (13%) -> umi_tools dedup I ...
written 4 weeks ago by Rituriya20

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Great Question 2.4 years ago, created a question with more than 5,000 views. For Collapse Probes For Same Gene
Popular Question 7.0 years ago, created a question with more than 1,000 views. For Collapse Probes For Same Gene

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