User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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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 5 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, Devon for your suggestions ...
written 5 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. 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 5 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 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 5 weeks 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 5 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by bioinforesearchquestions80
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Comment: C: What kind of filtering can be applied to reduce my exonic variants?
... Thanks, WouterDeCoster. Yeah, I am also going to run HaplotypeCaller (with GVCFs) individually for 3 samples and then run joint genotyping. I thought of taking the union of calls from Unified genotyper and HaplotypeCaller. I thought those calls might true positives. Does it make sense or not? I am ...
written 8 weeks ago by bioinforesearchquestions80
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What kind of filtering can be applied to reduce my exonic variants?
... Hi Folks, I am carrying out Exomeseq analysis for trio (**Son is affected, Father is affected, Mother is unaffected**). I did following steps - Trimmed using Trimmomatic - Aligned using BWA mem, Sorted, Marked Duplicates and Recalibrated. - For all 3 samples the coverage for target bases at 20X ...
exomeseq dnaseq trio snp variants written 8 weeks ago by bioinforesearchquestions80 • updated 7 weeks ago by Petr Ponomarenko2.3k

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Popular Question 23 days ago, created a question with more than 1,000 views. For Applying hard filters for variants
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Popular Question 7 months ago, created a question with more than 1,000 views. For Applying hard filters for variants

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