User: David_emir

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David_emir340
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Posts by David_emir

<prev • 151 results • page 1 of 16 • next >
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Validating Results from NMF Clustering & Consensus clustering
... Hi, I am running NMF/Consensus Clustering on my cancer samples and wanted it to cluster the samples into various subgroups, my question is how to conduct cluster assessment? Can I get P-value or something like that so that I can say my clustered samples are fine and validated? Regards, Dave ...
rna-seq validation written 22 days ago by David_emir340 • updated 21 days ago by anbarasu.la10
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Comment: C: What is the best pipeline for analyzing Non-invasive prenatal (NIPT) data?
... But, this is for fetal DNA quantification! Not exactly for identification of Trisomies. ...
written 11 weeks ago by David_emir340
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Comment: C: Aligning Multiple paired end files together
... Thanks a lot for your help, i am able to sucessfully run BWA on my .fastq files. with following code, for f in $(ls *.fq_filtered | sed -e 's/_1.fq_filtered//' -e 's/_2.fq_filtered//' | sort -u) do bwa mem -t 20 hg19 ${f}_1.fq_filtered ${f}_2.fq_filtered > /path/to/be/saved/${f}.sam ...
written 12 weeks ago by David_emir340
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Comment: C: Aligning Multiple paired end files together
... Thanks for the reply, i have added my script, please have a look ...
written 12 weeks ago by David_emir340
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Aligning Multiple paired end files together
... Hi All, I have 72 paired end .fastq file for which i need to do Alignment using BWA. Since its a paired end data and my files are named as 1. sam_001_1.fastq 2. sam_001_2.fastq 3. sam_002_1.fastq 4. sam_002_2.fastq & so on Since its a paired end data i am not able to generate a single .s ...
assembly alignment bwa shell written 12 weeks ago by David_emir340
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Comment: C: NIPT for microdeletion and microduplication sydnromes
... Thanks a lot for your quick response. You mentioned about RAPIDr ... My question still remains valid, i did go through the git page. If you have missed, I'm looking for rapidr-plus package, I'm sure you will be having it, please share the link for all of us to download. Regards ...
written 3 months ago by David_emir340
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NIPT for microdeletion and microduplication sydnromes
... Hi, I am looking for a package which can for identification of microdeletion and microduplication sydnromes. I am not able to find RapidR-Plus package so that i can use the same for NIPT. Please let me know which will be the best/good pipeline for identification of trisomy and microdeletion and mic ...
rapidr microdeletion nipt written 3 months ago by David_emir340
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Comment: C: CNV detection for NIPT analysis
... Hi, Can you please share RAPIDR-PLUS software? I am not sure how to get this ? i can only find RAPIDR. Thanks ...
written 3 months ago by David_emir340
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Comment: C: ADVOCATE R package
... [It is here][1], Its Github repository. [1]: https://github.com/califano-lab/ADVOCATE ...
written 4 months ago by David_emir340
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ADVOCATE R package
... Hi All, I am using `ADVOCATE` R package to determine virtual expression from bulk gene expression. I am currently using TCGA-PAAD data. I have checked `ADVOCATE` manual, I am unable to understand the output generated. My question is how to interpret the output in this case? Can we use `ADVOCATE` tr ...
advocate R rna-seq written 4 months ago by David_emir340 • updated 3 months ago by kristoffer.vittingseerup2.0k

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