User: Prakki Rama

gravatar for Prakki Rama
Prakki Rama2.4k
Reputation:
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Location:
Singapore
Website:
https://asearchforsolu...
Twitter:
Prakki_Rama
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Google Scholar Page
Last seen:
5 months, 2 weeks ago
Joined:
8 years, 6 months ago
Email:
r***********@gmail.com

Senior Bioinformatician

Tan Tock Seng Hospital, Singapore

Linkedin: http://tiny.cc/fn92qy

Posts by Prakki Rama

<prev • 425 results • page 1 of 43 • next >
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Answer: C: Example NGS data
... Qiagen's website provides example Illumina data (fastq format) for Pseudomonas aeruginosa (616 MB). Can find the link to download data from the following link: https://www.qiagenbioinformatics.com/support/example-data/ Can start using cutadapt on this data first. ...
written 6 months ago by Prakki Rama2.4k
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Comment: C: Fasted method to intersect VCF files
... I would try to reduce search time by breaking the large vcf file into smaller vcf according to chromosome and search the records in 1 MB vcf file against the broken vcf files. With this, I am saving more time instead of searching 28 Gb vcf. ...
written 7 months ago by Prakki Rama2.4k
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Comment: C: Circos Plot for synteny relationship
... you can try SyMAP (less complicated than circos) which is used for the similar purpose - It can align a draft genome to a fully sequenced genome. For more details check: http://www.agcol.arizona.edu/software/symap/ ...
written 7 months ago by Prakki Rama2.4k
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Comment: C: CD-HIT Clustering output
... Hi @syed. I just saw your message. The above script has actually worked for me. Let me show you, how I did. $ cat test.fasta >Cluster 0 0 22431nt, wt1_800... * >Cluster 1 0 21560nt, mock2_6320... * >Cluster 2 0 2668nt, wt2_2859... at 99.06% 1 4470nt, ...
written 12 months ago by Prakki Rama2.4k
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Comment: C: Creating Interactive Volcano Plots with R and Plot.ly
... It works for me after little modification. I have put "" and for the object Fold and FDR, I have done something like this: p <- plot_ly(data = diff_df, x = diff_df$Fold, y = -log10(diff_df$FDR), text = "external_gene_name", mode = "markers", color = "group") ...
written 13 months ago by Prakki Rama2.4k
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Comment: C: Filtering VCF file
... Hi it is here: https://mbio.asm.org/content/7/2/e02162-15 ...
written 13 months ago by Prakki Rama2.4k
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Comment: C: Replace the bases with N for the sites with evidence of a SNP
... Hi. As I have stated in my question, there are if conditions which I need to fulfill before I replace the gaps with either N or Reference base. Simply using bedtools maskfasta might not accomplish what I need. I would be glad to accept and vote your answer if you can actually post your steps to solv ...
written 13 months ago by Prakki Rama2.4k
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Answer: A: Replace the bases with N for the sites with evidence of a SNP
... Answering the question myself. I have written a perl script which can actually do this. It can be found in [github][1] for reference. [1]: https://github.com/ramadatta/Scripts/blob/master/perl/replaceAmbigousBases2N.pl ...
written 13 months ago by Prakki Rama2.4k
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Comment: C: Replace the bases with N for the sites with evidence of a SNP
... Hi @Pramod. Thank you. But as mentioned in the question, I am looking to replace Ns if only a SNP is present in the whole column and it is slightly beyond just matching a pattern and replacing it. I might end up writing my own script for this. Just did not want to reinvent the wheel. Anyways, thank ...
written 13 months ago by Prakki Rama2.4k
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Comment: C: Replace the bases with N for the sites with evidence of a SNP
... Hi @abedkurdi10. Thank you. I understand bedtools maskfasta can mask the base to N's but I am looking for some tool or script which can replace N only when there is a SNP in the whole column as mentioned in my question. ...
written 13 months ago by Prakki Rama2.4k

Latest awards to Prakki Rama

Great Question 6 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Popular Question 6 months ago, created a question with more than 1,000 views. For Status of maker annotation
Scholar 7 months ago, created an answer that has been accepted. For A: [Noob Doubt] Mapping and Annotation.
Scholar 7 months ago, created an answer that has been accepted. For A: Sub sampling from pyrosequencing reads
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Scholar 13 months ago, created an answer that has been accepted. For A: Sub sampling from pyrosequencing reads
Student 15 months ago, asked a question with at least 3 up-votes. For Must know algorithms before attending a bioinformatics interview
Great Question 17 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Popular Question 18 months ago, created a question with more than 1,000 views. For Status of maker annotation
Great Question 23 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Epic Question 2.9 years ago, created a question with more than 10,000 views. For Aligning Reads To A Reference Transcriptome
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Assessing The Quality Of De Novo Assembled Data
Student 3.2 years ago, asked a question with at least 3 up-votes. For Assessing The Quality Of De Novo Assembled Data
Epic Question 3.2 years ago, created a question with more than 10,000 views. For Assessing The Quality Of De Novo Assembled Data
Librarian 3.2 years ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Meaning of Chromatin state

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