User: Prasad

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Prasad1.6k
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India
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Posts by Prasad

<prev • 219 results • page 1 of 22 • next >
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Answer: C: conversion of genes sequence in protein sequence
... Have you tried [TransDecoder][1] [1]: https://github.com/TransDecoder/TransDecoder/wiki ...
written 22 months ago by Prasad1.6k
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Comment: C: Is bowtie adopting AI to become smarter !! :P
... True. I wanted to have quick view on the data so choose bowtie, when % was only 53 then i went for splice aligners (tophat and hisat) those results were much lesser (was expecting it to be better than bowtie). When i checked unaligned, they are still matching to jujube. is it the data which is a que ...
written 24 months ago by Prasad1.6k
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Comment: C: Is bowtie adopting AI to become smarter !!
... I was just curious to know how bowtie performed better than splice aware aligners. header i meant in fun way ...
written 24 months ago by Prasad1.6k
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Is bowtie adopting AI to become smarter !! :P
... Hi all, I have come across very peculiar alignment results for plant RNASeq data. I have aligned RNASeq data 150 *2 illumina stranded library [think matters only during expression quantification]. Aligned to its reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCA_000826755.1) using bowtie2, ...
alignment rna-seq written 24 months ago by Prasad1.6k
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Comment: C: RNA seq samtools flagstat
... Tophat by default gives only aligned reads as accepted.bam but not star. You may have checked accepted.bam hence the difference. Look at total reads from both they are different ...
written 24 months ago by Prasad1.6k
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Comment: C: How to extract Gene sequence from a fasta file using Cufflink ID?
... Have you tried `gffread` or `fastafrombed`. Gffread has options to extract only coding region or proteins many more from gff/gtf ...
written 2.0 years ago by Prasad1.6k
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Comment: C: local blastn against one subgroup of species
... Rebuild the db only for subset of your interest. If this is not feasible just restrict blast search using -gilist by providing gi ids of subset sequence. Refer to the manual on detailed explanation ...
written 2.0 years ago by Prasad1.6k
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Comment: C: Converting gene ids to each other
... Yes gene ID is same as Entrez gene ID ...
written 2.5 years ago by Prasad1.6k
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Answer: A: Converting gene ids to each other
... biodbnet has many option. for conversion db2db https://biodbnet-abcc.ncifcrf.gov/db/db2db.php ...
written 2.5 years ago by Prasad1.6k
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Comment: C: SpliceR visualization tool
... Tried but couldn't get the desire result means failed to visualize splicing events what was reported. ...
written 2.6 years ago by Prasad1.6k

Latest awards to Prasad

Popular Question 22 months ago, created a question with more than 1,000 views. For Gene Ontology categorization
Popular Question 23 months ago, created a question with more than 1,000 views. For Samtool Pileup output format
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: searching for sequences in a fastq file
Popular Question 2.6 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 2.7 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 2.9 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 3.1 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 3.1 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Precursor identification of mature miRNA
Guru 3.2 years ago, received more than 100 upvotes.
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Handbook(s) for Bioinformatics Ninjas
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Novel miRNA taregt gene prediction tool?
Scholar 3.2 years ago, created an answer that has been accepted. For A: Finding orthologous gene within species
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Handbook(s) for Bioinformatics Ninjas
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: searching for sequences in a fastq file
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: PERL: how to print specific length of residues before and after a motif?
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Regarding differentially expressed genes analysis
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: blastn for short sequences against a genome
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Novel miRNA taregt gene prediction tool?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Genome comparison using BRIG
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Where can i get library.txt file for SSPACE?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For C: How to sort chromosome name in bed file
Student 3.2 years ago, asked a question with at least 3 up-votes. For Type of inhibition between miRNA-mRNA
Student 3.2 years ago, asked a question with at least 3 up-votes. For NCBI feature table sequence extraction
Student 3.2 years ago, asked a question with at least 3 up-votes. For RAP-Seq : CDR region prediction

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