User: Aamiralizai

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Posts by Aamiralizai

<prev • 11 results • page 1 of 2 • next >
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Mendelian randomization analysis - OR and Beta value
... Hello everyone, I am doing Mendelian randomization analysis, I have extracted SNPs of one GWAS data from another GWAS data. I wanna find the effect of one SNPs set on another for which I wanna combine SNPs-exposure and SNPs-outcome via inverse-variance-weighted approach but the problem is that one ...
or mendelain randomization beta written 2.5 years ago by Aamiralizai0 • updated 2.3 years ago by RamRS25k
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Finding Bacterial % composition from Blast+ result
... Hello Everyone, i am interesting to get the percentage of a bacterial species from Blast result i am using greengene database for blast, i blast my file against the green gene database now i want to extract information and the percentage composition of each hit like shown in figure ........ Pleas ...
genome alignment blast sequencing written 3.4 years ago by Aamiralizai0 • updated 3.4 years ago by igor9.6k
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Comment: C: Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid [
... Hi Devon Ryan i think there is no problem with my sorted.bam because i used this file for GATKs to call SNPs ...
written 3.5 years ago by Aamiralizai0
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Comment: C: Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid [
... No it give a vcf file having 3k which having following info and then stopped ##fileformat=VCFv4.2 ##FILTER= ##samtoolsVersion=1.3.1+htslib-1.3.1 ##samtoolsCommand=samtools mpileup -d8000 -ugf /lustre/home/bioxsyy/DATABASE/hg19.fa /lustre/home/bioxsyy/Aamir/data/1.sorted.bam ##r ...
written 3.5 years ago by Aamiralizai0 • updated 3.5 years ago by Devon Ryan94k
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Comment: C: [mpileup] 1 samples in 1 input files Is it an error?
... [enter link description here][1] [1]: https://www.biostars.org/p/182517/#207184 ...
written 3.5 years ago by Aamiralizai0
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Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files
... Hello everyone i am facing a problem while run a command to call variant, i am using sorted.bam file (generated by picard-tools-1.119) $SOFTWARE/samtools mpileup -d8000 -ugf $DATABASE/hg19.fa $DATA/1.sorted.bam |$SOFTWARE1/bcftools call -m |$SOFTWARE1/vcfutils.pl varFilter -Q 20 - > samtool ...
snp written 3.5 years ago by Aamiralizai0 • updated 2.7 years ago by Istvan Albert ♦♦ 82k
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Comment: C: [mpileup] 1 samples in 1 input files Is it an error?
... But i didn't got vcf file the error file show this message, and the process fail further ...
written 3.5 years ago by Aamiralizai0
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Comment: C: [mpileup] 1 samples in 1 input files Is it an error?
... Hello everyone i also having same problem please anyone can help i am using sorted.bam file to call variants ...
written 3.5 years ago by Aamiralizai0
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Answer: A: Picard MarkDuplicates VM warning: fix the library
... https://www.raspberrypi.org/forums/viewtopic.php?f=81&t=146784 ...
written 3.7 years ago by Aamiralizai0
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Answer: A: Picard MarkDuplicates VM warning: fix the library
... https://www.raspberrypi.org/forums/viewtopic.php?f=81&t=146784 ...
written 3.7 years ago by Aamiralizai0

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