User: Prakki Rama

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Prakki Rama2.3k
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Location:
Singapore
Website:
https://asearchforsolu...
Twitter:
Prakki_Rama
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Last seen:
1 month, 2 weeks ago
Joined:
7 years, 4 months ago
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r***********@gmail.com

Bioinformatics Research Associate 

Linkedin: http://tiny.cc/fn92qy

Posts by Prakki Rama

<prev • 414 results • page 1 of 42 • next >
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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 weeks 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 weeks ago by Prakki Rama2.3k
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Filtering VCF file
... Hi all, I am trying to filter VCF file based on a publication with the following criteria. Base calls derived from these two Vcf files were then retained only if **(1) the proportion of high-quality bases supporting the call was ⱖ90%,** Is this same as setting `DP4/DP` >= 90%? **(2) 5 hig ...
vcf snp filtering written 8 weeks ago by Prakki Rama2.3k • updated 17 days ago by Biostar ♦♦ 20
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Comment: C: How do I access genome coverage using SPADES?
... Thx! BBMAP was very helpful! ...
written 4 months ago by Prakki Rama2.3k
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Comment: C: Error using in Smalt aligner program
... It is a bug that is fixed in 0.7.6 version. From the SMALT release history: > - fixed bug in 'smalt map -p' resulting in the "assertion failed" error message. This could occur when a read aligned across two successive sequences in the reference file for which the index was > constructed, ...
written 6 months ago by Prakki Rama2.3k
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Comment: C: Tool for calculating sequence statistic values (e.g. N50) for multiple bins
... Hi Brian, Just a comment. I used the wrapper you mentioned above. I get the output as following: Main genome scaffold N/L50: 3/804334 Main genome contig N/L50: 3/804334 It appears N and L values should be other way around : `N/L50: 804334/3` ...
written 6 months ago by Prakki Rama2.3k
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Comment: C: Missing sequences in local NT database
... Actually, this is not straight forward. Downloading large files is timing out. So, for now, I just used NCBI eutils to download my sequence from NCBI online: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sequences&id=NC_019090.1&rettype=fasta&retmode=text This also ...
written 7 months ago by Prakki Rama2.3k
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Comment: C: Missing sequences in local NT database
... @gb These are [merged data entries][1] in NCBI databases. [1]: http://asearchforsolutions.blogspot.com/2018/02/merged-entries-in-non-redundant.html ...
written 8 months ago by Prakki Rama2.3k
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Comment: C: Missing sequences in local NT database
... Sure Thanks much @lieven !! I will try it and post again! ...
written 8 months ago by Prakki Rama2.3k
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Comment: C: Missing sequences in local NT database
... I am trying to download fasta file from FTP. But, connection is timed out. I also tried downloading using axel from terminal. Still had the same problem. Any other ideas to access the fasta sequence data? ...
written 8 months ago by Prakki Rama2.3k

Latest awards to Prakki Rama

Great Question 3 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Popular Question 4 months ago, created a question with more than 1,000 views. For Status of maker annotation
Great Question 9 months ago, created a question with more than 5,000 views. For Meaning of Chromatin state
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 16 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Popular Question 17 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: [Noob Doubt] Mapping and Annotation.
Popular Question 19 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Epic Question 20 months ago, created a question with more than 10,000 views. For Aligning Reads To A Reference Transcriptome
Popular Question 22 months ago, created a question with more than 1,000 views. For How to generate AGP format using contigs and scaffolds
Epic Question 2.1 years ago, created a question with more than 10,000 views. For Assessing The Quality Of De Novo Assembled Data
Librarian 2.1 years ago, created a post with more than 10 bookmarks. For Assessing The Quality Of De Novo Assembled Data
Student 2.1 years ago, asked a question with at least 3 up-votes. For Assessing The Quality Of De Novo Assembled Data
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Assessing The Quality Of De Novo Assembled Data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Meaning of Chromatin state
Popular Question 2.2 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 2.2 years ago, created a question with more than 1,000 views. For #Reads Per Contig Information From Assemblies Other Than Velvet
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: samtools idxstats on indexed BAM failed
Great Question 2.3 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 2.7 years ago, created a post with more than 20 followers. 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 Quickest way to extract subset of reads from huge fastq file
Scholar 2.8 years ago, created an answer that has been accepted. For A: RNAseq: remove contaminants before or after mapping reads?
Appreciated 2.9 years ago, created a post with more than 5 votes. For Assessing The Quality Of De Novo Assembled Data

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