User: cvu

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

<prev • 63 results • page 1 of 7 • next >
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Answer: A: run gene enrichment analysis using metatranscriptomic data
... Did you resolve this problem? which OrgDb can be used? ...
written 5 months ago by cvu110
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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 months 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 7 months ago by cvu110 • updated 6 months 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 11 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 11 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 11 months ago by cvu110 • updated 11 months ago by Macspider2.5k
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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 13 months ago by cvu110
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Comment: C: Predict Prion like Proteins (PLAAC)
... Thanks for the reply microfuge ...
written 13 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 13 months ago by cvu110 • updated 13 months ago by Samuel Brady240
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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 13 months ago by cvu110 • updated 12 months ago by Biostar ♦♦ 20

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