User: BAGeno

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BAGeno130
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Posts by BAGeno

<prev • 69 results • page 1 of 7 • next >
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Control Samples for Excavator
... Hi, I want to find copy number variation in my samples. Samples are of psychiatry patients and I have done exome sequencing on NextSeq. For this purpose I want analyse samples with excavator. The problem is choosing control sample for this analysis. Can I choose ExAC samples? Will it be right to ch ...
excavator cnv written 12 weeks ago by BAGeno130
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GATK PrintRead Producing Empty File
... Hi, I am running gatk command on human chr21 which I downloaded from UCSC. I have performed alignment with `bwa`. Then sorted, marked duplicates and added read groups with `Picard` tool. After I perform base quality score recalibration with `gatk`. But when I performed `printreads` step it produced ...
gatk printread written 3 months ago by BAGeno130 • updated 3 months ago by Pierre Lindenbaum121k
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Comment: C: Need sample vcf file containing Complete Exome sequences
... you can download whole exome files from gnomAD site. ...
written 3 months ago by BAGeno130
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Comment: C: SNps and calculation of sample size
... You can write dbSNP or ensemble and see if gene has SNP or not. ...
written 3 months ago by BAGeno130
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Comment: C: Whole Exome CNV tools
... Thanks for your suggestion but VarScan is for tumor normal pair exome data. My patients are not cancer patients. ...
written 3 months ago by BAGeno130
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Whole Exome CNV tools
... Hi, I want to ask that can we use breakerdancer, manta,delly, lumpy-sv for copy number variation calling of whole exome analysis? I have just whole exome data of five patients and I want to call their copy number variations. ...
exome next-gen cnv sequencing written 3 months ago by BAGeno130 • updated 3 months ago by ReWeeda50
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(Closed) Illumina NextSeq shorter fragment size than expected
... Hi, We were preparing library for NextSeq whole exome sequencing. Our starting concentration before library preparation for three samples were 27ng/µL, 37ng/µL and 42ng/µL. We pooled library and when we checked our fragment size before running on sequencer by Bioanalyzer, we saw fragment size of 23 ...
illumina next-gen sequencing written 4 months ago by BAGeno130
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Failed to liftover from hg38 to hg19
... Hi, I am converting my file from hg38 to hg19. For this purpose I used `crossmap` and `picard LiftoverVcf`. But I am getting this error when I run `crossmap`. Traceback (most recent call last): File "/home/linux/anaconda3/bin/CrossMap.py", line 1760, in crossmap_vcf_file(mapping ...
crossmap picard written 6 months ago by BAGeno130
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Annovar and VEP overlapp
... Hi, I want to check VEP and annovar overlap that is how many variants are annotated same by both of these tools. But I don't how to do it as VEP output contain many transcripts and so there is difference in number of annotations done by both these tools. So what do you suggest I should perform the ...
annovar vep written 6 months ago by BAGeno130 • updated 6 months ago by Kevin Blighe44k
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Comment: C: Vep loftool threshold
... I want to separate probably damaging variants from output. So what value should I used to separate these variants? ...
written 6 months ago by BAGeno130

Latest awards to BAGeno

Popular Question 5 months ago, created a question with more than 1,000 views. For EBI SRA FTP is not working
Popular Question 7 months ago, created a question with more than 1,000 views. For VEP and Annovar Annotation
Popular Question 8 months ago, created a question with more than 1,000 views. For Grep Position List

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