User: cvu

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cvu140
Reputation:
140
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India
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8 months, 3 weeks ago
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Posts by cvu

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Removing columns coded by -,N or ? in Alignments
... You can use `sed` command if you just want to remove these characters `sed 's/[N|?|-]//g' filename` ...
written 10 months ago by cvu140
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Remove Sequences from existing Bowtie2 index
... Hello All, I've created a bowtie2 large index, Which is a huge data set (~100GB) it took approx 2days to generate a bowtie2 index. Now I came across problems with some sequences and I want to remove it from my existing index. Is there a way to remove sequences based on their identifiers directly ...
genome bowtie2 ngs index written 10 months ago by cvu140
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Answer: A: run gene enrichment analysis using metatranscriptomic data
... Did you resolve this problem? which OrgDb can be used? ...
written 17 months ago by cvu140
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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 19 months ago by cvu140
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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 20 months ago by cvu140 • updated 18 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 23 months ago by cvu140
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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 23 months ago by cvu140
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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 23 months ago by cvu140 • updated 23 months ago by Macspider2.8k
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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 2.1 years ago by cvu140
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Comment: C: Predict Prion like Proteins (PLAAC)
... Thanks for the reply microfuge ...
written 2.1 years ago by cvu140

Latest awards to cvu

Scholar 14 months ago, created an answer that has been accepted. For A: how i can install bowtie?
Popular Question 17 months ago, created a question with more than 1,000 views. For how to map greengene ids to ncbi taxon ids ?
Great Question 19 months ago, created a question with more than 5,000 views. For Creating reference Index using Bowtie2
Epic Question 23 months ago, created a question with more than 10,000 views. For Bowtie2 parameters for best alignment
Popular Question 23 months ago, created a question with more than 1,000 views. For VariantRecalibrator Error message
Supporter 2.1 years ago, voted at least 25 times.
Great Question 2.1 years ago, created a question with more than 5,000 views. For Creating reference Index using Bowtie2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For VariantRecalibrator Error message
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Samtools mpileup refrence fasta file input
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Give hyperlink to pdf table perl
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Comparing vcf with dbSNP
Great Question 3.4 years ago, created a question with more than 5,000 views. For Bowtie2 parameters for best alignment
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Comparing vcf with dbSNP
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Bowtie2 parameters for best alignment
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Bowtie2 parameters for best alignment

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