User: Prakki Rama

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Prakki Rama2.3k
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Singapore
Website:
https://asearchforsolu...
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Prakki_Rama
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Last seen:
2 weeks, 2 days ago
Joined:
7 years, 10 months ago
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r***********@gmail.com

Bioinformatics Research Associate 

Linkedin: http://tiny.cc/fn92qy

Posts by Prakki Rama

<prev • 422 results • page 1 of 43 • next >
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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 4 months ago by Prakki Rama2.3k
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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 5 months ago by Prakki Rama2.3k
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Comment: C: Filtering VCF file
... Hi it is here: https://mbio.asm.org/content/7/2/e02162-15 ...
written 5 months ago by Prakki Rama2.3k
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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 5 months ago by Prakki Rama2.3k
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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 5 months ago by Prakki Rama2.3k
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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 5 months ago by Prakki Rama2.3k
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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 5 months ago by Prakki Rama2.3k
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Replace the bases with N for the sites with evidence of a SNP
... Hi all, I have a alignment fasta file which looks like this: $ cat alignment_file.fasta >Ref1 ATCG >S1 AT-C >S2 CTCG >S3 ATCG >S4 -TCG Specifically, what I want is: 1) If there exists a SNP (for eg: "C" in the S2 sequence in the position ...
alignment snp written 5 months ago by Prakki Rama2.3k • updated 5 months ago by chantelmarshal3210
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Comment: C: Annotating/Finding "NNNNNN" scaffold gaps in genome assembly
... perl [one-liner][1] to do this. [1]: https://www.biostars.org/p/133742/#377084 ...
written 7 months ago by Prakki Rama2.3k
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Comment: C: How to extract all non-seqenced positions from a genome (Fasta file)?
... After 4.1 years... Hi @mxs, thanks for the script. For some reason, I was getting an error in the result. I modified your script slightly. Below are the steps: $ cat test2.txt >NZ_CP025963.1 ATGCAGTNNNACGTGCATGACTGTACGTANGTACGTGACTGACTGACTGACTNACTGACTGATCGTACNTACGTAC $ perl -ne ...
written 7 months ago by Prakki Rama2.3k

Latest awards to Prakki Rama

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Scholar 5 months ago, created an answer that has been accepted. For A: Sub sampling from pyrosequencing reads
Student 7 months ago, asked a question with at least 3 up-votes. For Must know algorithms before attending a bioinformatics interview
Great Question 9 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Popular Question 10 months ago, created a question with more than 1,000 views. For Status of maker annotation
Great Question 15 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 22 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Popular Question 22 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Aligning Reads To A Reference Transcriptome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Assessing The Quality Of De Novo Assembled Data
Librarian 2.6 years ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Student 2.6 years ago, asked a question with at least 3 up-votes. For Assessing The Quality Of De Novo Assembled Data
Epic Question 2.6 years ago, created a question with more than 10,000 views. For Assessing The Quality Of De Novo Assembled Data
Popular Question 2.7 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 2.7 years ago, created a question with more than 1,000 views. For Meaning of Chromatin state
Popular Question 2.7 years ago, created a question with more than 1,000 views. For #Reads Per Contig Information From Assemblies Other Than Velvet
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: samtools idxstats on indexed BAM failed
Great Question 2.8 years ago, created a question with more than 5,000 views. For Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant
Prophet 3.1 years ago, created a post with more than 20 followers. For Assessing The Quality Of De Novo Assembled Data

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