User: cvu

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cvu110
Reputation:
110
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India
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1 week, 4 days ago
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3 years, 9 months ago
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Posts by cvu

<prev • 62 results • page 1 of 7 • next >
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bsseq fisherTest result
... Hi all, I've performed fisherTests() function of bsseq bioconductor package for two samples since I've only one replicate for each samples. but fishertest result gives only two columns p.value and log2OR and I want to know its corresponding chromosome and position information. also I want to filter ...
bsseq methylation bisulfite sequencing written 7 weeks ago by cvu110
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RRBS: import Bismark output to RnBeads
... Hello All, I am running Bisulfide sequencing samples. I've directional libraries with four single-ended fastq files for each sample and completed with bismark and got four bam files which i've merged and finally got one bam file for each sample. These are the commands I ran: bismark --genome_ ...
bsseq methylation bismark bisulfite sequencing written 8 weeks ago by cvu110 • updated 25 days ago by Biostar ♦♦ 20
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Comment: C: standalone BLAST parametes
... Thanks for the reply. I want only one best match for each protein, Hence I set hsp 1. ...
written 5 months ago by cvu110
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Comment: C: standalone BLAST parametes
... Thanks for the reply. I want perfect matches, but which parameters to set to get a good match? ...
written 5 months ago by cvu110
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standalone BLAST parametes
... Hi All, I've predicted genes in genome. Now I want to identify proteins, For that, I've blasted all predicted proteins against uniprot database. blast parameters blastp -query proteins.fasta -db Uniprotdb -max_target_seqs 1 -max_hsps 1 -out output.blastp -outfmt 6 -evalue 0.001 what should b ...
genome gene blast written 5 months ago by cvu110 • updated 5 months ago by Macspider2.2k
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Comment: C: which tool is used for separating forward and reverse from paired end fastq
... use SRA Toolkit https://www.ncbi.nlm.nih.gov/books/NBK158900/ and use fastq-dump, for example `fastq-dump -I --split-files SRR390728` to split paired end reads. ...
written 7 months ago by cvu110
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Comment: C: Predict Prion like Proteins (PLAAC)
... Thanks for the reply microfuge ...
written 7 months ago by cvu110
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Intronic Variant Filtering
... Hello all, I want to filter variants based on their genomic location. For example RSID rs10863805, this variant is Intronic variant and it is 18 nucleotides away from exon and I want to keep all intronic variants which falls in before or after 100 nucleotides of exon region. > 5'-------INTRON ...
intron snp variantcalling written 7 months ago by cvu110 • updated 7 months ago by Samuel Brady230
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Predict Prion like Proteins (PLAAC)
... Hi All, I'm using PLAAC (http://plaac.wi.mit.edu/) to identify probable prion subsequences in my protein sequences. but I get different LLR scores for same protein sequence, when I give fasta and multifasta files. Output from FASTA file SEQid MW MWstart MWend MWlen LLR LLRstar ...
gene prion protein written 7 months ago by cvu110 • updated 6 months ago by Biostar ♦♦ 20
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RAD-seq Downstream analysis
... Hello People, I am new to RAD-seq analysis and I've 100 samples of RAD-seq paired end double digest data from single population. I ran ipyrad and have got different output formats (vcf, loci, geno, phy, str etc.). Now I'm not able to generate graphs. I want to do qtl mapping, parsimony analysis, ph ...
rad-seq ipyrad downstream written 8 months ago by cvu110 • updated 3 hours ago by pbpearman0

Latest awards to cvu

Great Question 7 weeks ago, created a question with more than 5,000 views. For Creating reference Index using Bowtie2
Epic Question 5 months ago, created a question with more than 10,000 views. For Bowtie2 parameters for best alignment
Popular Question 5 months ago, created a question with more than 1,000 views. For VariantRecalibrator Error message
Supporter 7 months ago, voted at least 25 times.
Great Question 7 months ago, created a question with more than 5,000 views. For Creating reference Index using Bowtie2
Popular Question 14 months ago, created a question with more than 1,000 views. For VariantRecalibrator Error message
Popular Question 14 months ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 14 months ago, created a question with more than 1,000 views. For Samtools mpileup refrence fasta file input
Popular Question 15 months ago, created a question with more than 1,000 views. For Give hyperlink to pdf table perl
Popular Question 18 months ago, created a question with more than 1,000 views. For Comparing vcf with dbSNP
Great Question 23 months ago, created a question with more than 5,000 views. For Bowtie2 parameters for best alignment
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Comparing vcf with dbSNP
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Bowtie2 parameters for best alignment
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Bowtie2 parameters for best alignment

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