User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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How to compare genotype calls of the SNPS on chrom X for the GWAS samples between plink file vs Affymetrix genotype output file?
... Hello friends, How to compare the genotype calls of the SNPs on chromosome X for the GWAS samples between the GWAS Plink file and the Affymetrix genotype output file to confirm whether the chromosome X genotype calls are 100% identical in the two files? He provided me sample sheet (sample-well pos ...
gwas affymetrix plink ped genotype written 18 days ago by bioinforesearchquestions80 • updated 4 days ago by Biostar ♦♦ 20
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Is there any tool to extract LD SNPs based on any other databases (except 1K database)?
... Hello friends, I am trying to extract LD SNPs for 10 rsids in CEU population. I tried using Haploreg "http://archive.broadinstitute.org/mammals/haploreg/haploreg.php" to extract LD SNPs but I couldn't get any for my list. I believe Haploreg is based on 1000 Genome database. Is there any other tool ...
ld snps 1000genome mutations written 6 weeks ago by bioinforesearchquestions80
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Comment: C: When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has
... Thanks, Jrj.healey. Just now, I did it. ...
written 3 months ago by bioinforesearchquestions80
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Comment: C: When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has
... Thanks, Devon for your suggestions ...
written 3 months ago by bioinforesearchquestions80
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Comment: C: When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has
... Thanks, Jrj.healey. To test this, I tried copying the BAM file to my local machine from the remote server. I could see the 9GB BAM file in my local machine :) ...
written 3 months ago by bioinforesearchquestions80
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Comment: C: When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has
... Thanks WouterDecoster. I have a Mac OS machine. I used both 128GB usb drive and 500GB hard disk, by default it has been formatted on MS-DOS (FAT32). Now I get it. I forgot to reformat the new drive and disk. ...
written 3 months ago by bioinforesearchquestions80
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When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has only 4GB.What could be the issue?
... Hello friends, I have multiple BAM files in my server, each of them is 9GB file. When I am trying to copy them to the hard disk, the copied BAM file has only 4GB. I tried multiple times, what could be the issue? When I opened the BAM file, I could see alignment only till chr8. ...
dnaseq alignment bam written 3 months ago by bioinforesearchquestions80
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Comment: C: What kind of filtering can be applied to reduce my exonic variants?
... Hi Petr Ponomarenko, This is a clinical as well as research study. Sure, I will try ALAPY and give my feedback on it. ...
written 3 months ago by bioinforesearchquestions80
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Comment: C: Tips for miRNA-Seq analysis
... Hi Jonessara, Even I have started working on miRNA recently. I am pretty much new to this analysis. 1) Generally, miRNA will be 15 to 35 bases in length. I hope you might have generated at least 51 bases from the sequencing machine. So make sure you trim the 3'end of the sequenced reads where you ...
written 3 months ago by bioinforesearchquestions80
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Answer: A: What kind of filtering can be applied to reduce my exonic variants?
... Sorry, I meant intersection, not union. "Haplotypecaller" is recommended by GATK team. Last week, I ran my 3 samples individually using "Haplotypecaller" with GVCF option. It failed 6 times due to memory issue. So that's the reason I first tried with "Unified Genotyper". But now I have used other hi ...
written 3 months ago by bioinforesearchquestions80

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