User: nilakshafreezon

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Sri Lanka
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Posts by nilakshafreezon

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Coverage analysis of NGS data by Depth
... I have human Exome data aligned to the GrCh37 reference as BAM files. Enriched regions are also available as a bed file. I need to get, up to what percentage the "supposed to be enriched regions" are actually covered and in what depth. For ex: Coverage at 10x = 95% Coverage at 20x = 90% Coverage a ...
written 2.3 years ago by nilakshafreezon110
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Coverage analysis of NGS data by Depth
... Hello, Can anybody please tell me a method to calculate the coverage of a NGS sequencing result (BAM File) given the sequence depth. ? For example; For sample 1 : Coverage at 10x = 95% Coverage at 20x = 90% Coverage at 30x = 86% etc. I've seen these kind of reports in Illumina M ...
ngs panels coverage depth written 2.3 years ago by nilakshafreezon110 • updated 2.1 years ago by lethanhx2k10
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Comment: C: Filterout biallelic SNPs from multiple VCF files.
... Thanks a lot. Is merging over 500 samples feasible? ...
written 4.9 years ago by nilakshafreezon110
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Filterout biallelic SNPs from multiple VCF files.
... Hi, I have a list of vcf files, one per each individual with the variants called for HLA genes. HLA has a lot of multi allelic SNPs but in this case I need to filter out only the biallelic SNPs, scanning through all vcf files. Is there any specific tool for this? Ex: sample 1 rs-xx G C sample 1 rs- ...
vcf hla bi allelic snp written 4.9 years ago by nilakshafreezon110 • updated 4.9 years ago by Adam990
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Comment: C: Efficient strategy for remote blasting of 3000 sequences
... Install galaxy locally on your computer. Install Blast+ locally as well. Then download and install Blast+ wrappers for galaxy. Then use galaxy to automate your blast. I just gave you the general overview. Find your way own. That's not hard. Let me know if u got any problem ...
written 5.2 years ago by nilakshafreezon110
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Comment: C: HLA typing analysis with plink or any other method?
... Thanks for the information :) ...
written 5.2 years ago by nilakshafreezon110
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Comment: C: HLA typing analysis with plink or any other method?
... Seems interesting. I will take a closer look. But not sure whether It can be used in the analysis except for missing allele imputation. Thanks :)   ...
written 5.2 years ago by nilakshafreezon110
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HLA typing analysis with plink or any other method?
... Hi, I have a set of HLA variants from a case control study annotated in tabulated files. I thought of analyzing them with plink and after a hard work, I tried to convert my raw data to plink supporting file formats. (.lgen,.map and .fam). Thought everything went smooth, but when I tried to run my da ...
hla plink written 5.2 years ago by nilakshafreezon110 • updated 5.2 years ago by Katie D'Aco1000
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Comment: C: pathway analysis tools
... I hope so, Im not quite sure though. That's why I gave it as an option so you could check out for your self. ...
written 5.2 years ago by nilakshafreezon110
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Comment: C: multisample BED files to PED conversion
... I was able to convert the files to TPED using a bash script. Only problem is that, I dont have any values for 2nd and 3rd fields (rs IDs and genetic distances) . Since the merge depends on the chromosome and position, (1st and 4th) as you said, I hope I won't get into any trouble when merging the fi ...
written 5.2 years ago by nilakshafreezon110

Latest awards to nilakshafreezon

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Filterout biallelic SNPs from multiple VCF files.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Filterout biallelic SNPs from multiple VCF files.
Popular Question 3.5 years ago, created a question with more than 1,000 views. For GATK: High quality value error
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Using A Cluster Of Macs To Share Computational Power
Popular Question 3.5 years ago, created a question with more than 1,000 views. For HLA typing analysis with plink or any other method?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Filterout biallelic SNPs from multiple VCF files.

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