User: bitpir

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bitpir10
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Posts by bitpir

<prev • 17 results • page 1 of 2 • next >
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Comment: C: do blast search using gi numbers
... Hi h.mon, I'm using rpsblast+ from blast+ package 2.5.0 and 2.6.0(latest). Yes, I suppose downloading fasta files will be the quickest solution, although my queries are rather large (>700K). NCBI's CD-search accept gi/accession number as query (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb ...
written 10 days ago by bitpir10
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Comment: C: do blast search using gi numbers
... Thank you for your response! Unfortunately, I didn't see any improvement when I converted my query from gi number to accession (eg EFL06024.1). The error regarding "Protein BLAST database 'Cog/Cog nr' does not exist in the NCBI servers" still there.... ...
written 10 days ago by bitpir10
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do blast search using gi numbers
... Hi, I'm trying to do an rpsblast using ncbi-blast-2.5.0+. I have a file containing gi numbers as my query and my command line is below. rpsblast -query t -db results/Cog/Cog -out rps-blast.out -evalue 1e-2 -outfmt 6 Oddly the rpbslast keeps giving me this error: Warning: [rpsblast] Error ...
blast written 10 days ago by bitpir10 • updated 10 days ago by piet1.4k
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finding NCBI protein ID and associated COG ID
... Hi there, I am new to the metagenomic field. I recently did a blastx of my contigs using the nr database. With the results, I plan to categorize the protein hits with COG_ID and COG functions. I am using the cog2003-2014.csv database that's available from the NCBI website, by looking up the protein ...
nr database blastx cog written 16 days ago by bitpir10
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Comment: C: customize reference genome
... Perfect, just what I need. Thanks! ...
written 20 days ago by bitpir10
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customize reference genome
... How do you customize a reference genome, say, hg19, and make into a personalized reference genome in fasta format? I don't have the phased sequence information, but I have the fastq's, bam, and vcf formats. ...
dna-seq written 21 days ago by bitpir10 • updated 21 days ago by WouterDeCoster20k
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software recommendations for identifying self from non-self dna sequences
... Hi there, I'm just wondering if there's a software out there that could help with identifying self from non-self dna sequences. I have the whole genome/wex dna sequences from an individual (self), and I also have a mixture of dna samples containing self and non-self (other individuals) samples. My g ...
forensics dna sequencing written 28 days ago by bitpir10
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Comment: C: Question about GATK hardfiltering conditions
... Thank you for the clarification! Using the OR option, variants that passes the filter will have QD > 2.0 and FS < 60.0 and MQ > 40.0 and MQRankSum > -12.5 and ReadPosRankSum > -8.0. ...
written 5 months ago by bitpir10
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Comment: C: Question about GATK hardfiltering conditions
... Thank you for the answer! I get it now, the OR option will filter out more variants than AND option. The filter expression is for variants that fail, as Vivek mentioned. My samples were not joint-called with a larger cohort upstream and therefore VQSR is not possible for my current sample set.... ...
written 5 months ago by bitpir10
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Question about GATK hardfiltering conditions
... Hello, GATK recommends the following filter expression for hard filtering of vcfs: "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" The website does explain where the numbers from each condition come from. However, I'm still trying to understand why ...
hardfiltering gatk written 5 months ago by bitpir10 • updated 5 months ago by Brian Bushnell13k

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Popular Question 5 months ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

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