User: cvu

gravatar for cvu
cvu110
Reputation:
110
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India
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5 hours ago
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3 years, 4 months ago
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Posts by cvu

<prev • 60 results • page 1 of 6 • next >
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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 4 days 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 4 days 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 4 days ago by cvu110 • updated 4 days ago by Macspider1.4k
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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 8 weeks ago by cvu110
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Comment: C: Predict Prion like Proteins (PLAAC)
... Thanks for the reply microfuge ...
written 9 weeks 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 9 weeks ago by cvu110 • updated 8 weeks 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 9 weeks ago by cvu110 • updated 5 weeks 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 12 weeks ago by cvu110
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Comment: C: joining paired end illumina data for metagenomic analysis
... can I put Ns between two reads to link them? it is 2x250 reads, and insert length is approximately 420. ...
written 3 months ago by cvu110
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Comment: C: joining paired end illumina data for metagenomic analysis
... thanks a lot genomax. I tried `bbmerge.sh` but got same result. ...
written 3 months ago by cvu110

Latest awards to cvu

Supporter 9 weeks ago, voted at least 25 times.
Great Question 11 weeks ago, created a question with more than 5,000 views. For Creating reference Index using Bowtie2
Popular Question 9 months ago, created a question with more than 1,000 views. For VariantRecalibrator Error message
Popular Question 9 months ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 9 months ago, created a question with more than 1,000 views. For Samtools mpileup refrence fasta file input
Popular Question 10 months ago, created a question with more than 1,000 views. For Give hyperlink to pdf table perl
Popular Question 13 months ago, created a question with more than 1,000 views. For Comparing vcf with dbSNP
Great Question 17 months ago, created a question with more than 5,000 views. For Bowtie2 parameters for best alignment
Popular Question 22 months ago, created a question with more than 1,000 views. For Comparing vcf with dbSNP
Popular Question 22 months ago, created a question with more than 1,000 views. For Creating reference Index using Bowtie2
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Bowtie2 parameters for best alignment
Popular Question 2.3 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 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

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