User: moushengxu

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moushengxu300
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Posts by moushengxu

<prev • 207 results • page 1 of 21 • next >
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How to resolve kinship with the software "king" using GWAS genotyping data?
... "king" can impute IBS0 and kinship coefficient using GWAS samples. It can generate Z0 (probability of IBD0) for within-family members but this is not common for a GWAS population. So how can you resolve the kinship using the king output file? For instance, how can you tell parent-child, monozygotic ...
snp written 9 days ago by moushengxu300
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Comment: C: How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
... We used RSEM to align and quantify the RNA-seq levels, and use estimated gene count = 5 as the threshold -- if none of the samples has gene count >= 5, that gene is filtered out and not used for downstream analysis. Unless you have a strong reason not to do so, this filtering method should serve ...
written 5 weeks ago by moushengxu300
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Comment: C: Can someone please help me run any GATK4 pipeline?
... java -jar cromwell-31.jar run germline_single_sample_workflow.wdl --inputs germline_single_sample_workflow.hg38.inputs.json ...
written 6 weeks ago by moushengxu300 • updated 6 weeks ago by Ram15k
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Comment: C: Can someone please help me run any GATK4 pipeline?
... I noticed that. I ran it on my MacBook Pro (MacOS 10.13.4), which should be the supported filesystem "MacOSXFileSystem" Do I have to do anything as described at http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems? ...
written 6 weeks ago by moushengxu300
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Can someone please help me run any GATK4 pipeline?
... GATK4 is a great variant calling software product and is dominating in the field. Unfortunately, I am not able to run any of the GATK4 pipelines, probably because these pipelines all use google storage which I am not familiar with? Now I am trying to run the $5 variant calling pipeline because I gue ...
software error next-gen snp sequencing written 6 weeks ago by moushengxu300 • updated 6 weeks ago by vdauwera780
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Comment: C: Where to find information on LD ~ distance?
... One more question: it looks like the they limited the distance between SNPs to be under 200kb, while at 200kb, there are still tons of significant LDs as the data can tell. I am not sure why they cut it off at 200kb and do not look beyond 200kb? ...
written 8 weeks ago by moushengxu300
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Comment: C: Where to find information on LD ~ distance?
... That is it! Thanks so much! ...
written 8 weeks ago by moushengxu300
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Where to find information on LD ~ distance?
... We want to know how far away Linkage Disequilibrium (LD) can go between SNPs, but I have difficulty locating such information. I checked out SNPsnap from Broad Institute at https://data.broadinstitute.org/mpg/snpsnap/database_download.html, but it actually does not have such information. Any help ...
genome snp written 8 weeks ago by moushengxu300
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Comment: C: GATK4 local computing workflow
... You are the best! I did post my questions to the GATK forum, but nobody answers me recently. A quick question: what are 2T, 56T, 20k, HDD, on-prem, throughputs, FPGA? A 2 cent suggestion: It would be nice to have a choice to automatically download all auxiliary datasets to designated directories ...
written 9 weeks ago by moushengxu300
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GATK4 local computing workflow
... We have a large sample size for WGS and variant calling, and now we are assessing different pipeline options. One of the pipelines we are investigating is the GATK4 pipeline. Broad provided a workflow defined in .WDL + JSON, but it uses cloud computing (reference files in the google storage cloud). ...
software error genome next-gen sequencing written 9 weeks ago by moushengxu300 • updated 9 weeks ago by vdauwera780

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