User: Prasad

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Prasad1.6k
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Posts by Prasad

<prev • 223 results • page 1 of 23 • next >
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Answer: A: Count all (non N) nucleotides within regions defined in BED file
... You can extract sequences for bed regions using "[getfasta][1]" followed by base counting using any of the options provided [here][2] [1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html [2]: https://www.biostars.org/p/353323/ ...
written 8 weeks ago by Prasad1.6k
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Comment: A: blastn many pairs of DNA sequences
... If you are not performing blind BLAST search (ex: against entire nr/nt), why not map using a read mapper (ex: bowtie) against reference sequences by taking these 2 files are paired data. This way you can also get an advantage of filtering out the mapping based on inner distance between each pair. ...
written 8 weeks ago by Prasad1.6k
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Comment: C: Trouble understanding "Join" operator of NCBI
... Yes, this is a circular genome and this gene goes past reference relative position (1), but 2 coordinates are overlapping making region 1820..1932 counted twice. Do we read this overlapping region only once when we make gene sequence linear? How to interpret this in gff3 as coordinates exceeds the ...
written 8 weeks ago by Prasad1.6k
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Trouble understanding "Join" operator of NCBI
... Hello, The Join operator is used for backsplicing events/split genes. Could anyone please provide additional details on interpretation of "Join" in case of pgRNA of NC_003977. In NC_003977, pgRNA (pre-genomic RNA; encodes core and polymerase) is denoted as join(1820..3182,1..1932) Why does p ...
ncbi gene gff3 written 8 weeks ago by Prasad1.6k • updated 8 weeks ago by Istvan Albert ♦♦ 86k
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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 3.1 years 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 3.2 years 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 3.2 years 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 3.2 years 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 3.2 years 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 3.2 years ago by Prasad1.6k

Latest awards to Prasad

Scholar 8 weeks ago, created an answer that has been accepted. For A: Finding orthologous gene within species
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Identify lncRNA in list of Ensemble ID's
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Error in Seqtk output
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Gene Ontology categorization
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bacterial morphology details
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Samtool Pileup output format
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Trinity: Merged assembly, Is it enough?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Prediction CRP binding sites
Popular Question 3.0 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Strange pattern in cufflink output
Popular Question 3.0 years ago, created a question with more than 1,000 views. For miRNA-Target coexpression and network
Popular Question 3.0 years ago, created a question with more than 1,000 views. For SpliceR visualization tool
Popular Question 3.0 years ago, created a question with more than 1,000 views. For 5c Analysis tool
Popular Question 3.0 years ago, created a question with more than 1,000 views. For DGE with PEER normalized data
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Precursor identification of mature miRNA
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Type of inhibition between miRNA-mRNA
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Tophat input ambiguity
Popular Question 3.0 years ago, created a question with more than 1,000 views. For RAP-Seq : CDR region prediction
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Gene Ontology categorization
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Samtool Pileup output format
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: searching for sequences in a fastq file
Popular Question 3.8 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 3.9 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 4.1 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs
Popular Question 4.2 years ago, created a question with more than 1,000 views. For functional analysis of intronic and neargene SNPs

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