User: David_emir

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David_emir250
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Posts by David_emir

<prev • 103 results • page 1 of 11 • next >
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Falcon Assembly error - [ERROR]Task Node(1-preads_ovl) failed with exit-code=256
... Hello All, I am having an error while running falcon assembler, the error is as follows, I am using Human reads. It would be really helpful if you can please help me. `**[ERROR]**Task Node(1-preads_ovl) failed with exit-code=256 [INFO]recently_satisfied: set([]) [INFO]Num satisfied in ...
falcon denovo written 9 days ago by David_emir250
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Comment: C: Differential methylation analysis
... Sorry for that. I have rectified it. Can you please let me know how to go about this? ...
written 18 days ago by David_emir250
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Differential methylation analysis
... Hello All, I am currently working on to understand the Methylation mechanism in Cancer condition. my area of study revolves around the mostly wet lab and I have basic knowledge about coding, here I need your help. I have two sets of samples from TCGA LUSC and LUAD samples. I want to do Differential ...
need tutorials written 18 days ago by David_emir250 • updated 17 days ago by mathias.heydt60
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Comment: C: Data Discrepency from TCGA-GDC portal and GDC firehose
... I was planning to Get Differential Gene Expression analysis done on raw count data (RNAseq data) for that i need to group the samples into various levels. ...
written 29 days ago by David_emir250
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Comment: C: Data Discrepency from TCGA-GDC portal and GDC firehose
... Thanks a lot or your help, Could you please let me know how to download the full ids? ...
written 29 days ago by David_emir250
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Data Discrepency from TCGA-GDC portal and GDC firehose
... Hello All, I was trying to get Lung cancer samples from TCGA (LUSC & LUAD). I wanted to categorize the data depending upon tumor stage. I have used the following command to download clinical file library("TCGAbiolinks") clinical_lusc <- GDCquery_clinic(project = "TCGA-LUSC", type = ...
firehose tcga gdc written 29 days ago by David_emir250 • updated 29 days ago by mbk0asis320
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Differentially methylated regions Analysis
... Hello All, I have TCGA data from RNAseq(Counts data) and DNA-Meth data. I am interested to conduct Differentially methylated regions Analysis on the same. I have tried working with TCGABioLinks package, and I am finding it difficult to execute and understand as well. After wasting about 2 months o ...
tcgabiolinks packages dmr written 5 weeks ago by David_emir250 • updated 5 weeks ago by noorpratap.singh90
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Comment: C: TCGABioLinks how to set Sample conditions?
... I am following the [tiagochst][1] code here, and i am finding it hard to replicate the same. i have given the samples which are Left and right (SetA and SetB) as follows, samplelist_left <- c("TCGA-A6-2671-01A", "TCGA-A6-2674-01A", "TCGA-A6-2674-01B", "TCGA-A6-2674-01A", "TCGA-A6-2675-01A", ...
written 5 weeks ago by David_emir250
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Comment: C: TCGABioLinks how to set Sample conditions?
... Thanks a lot for your suggestion, Mathias.heydt. It was indeed very helpful. I have set of samples which I have classified as Set A and Set B (Both are from Colon Cancer). Now the problem is, I just want to bypass the clinical classification since I am not classifying between Normal Vs tumor, instea ...
written 5 weeks ago by David_emir250
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Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... Hello All, I am in process of polishing an assembly produced by Falcon using arrow. However, it is failing with an error "Keyerror BASECALLERVERSION". These are the steps I followed: 1. pbalign reference.fasta falcon_draft_assembly.fa --nproc 32 quvir.sam 2. samtools view -bS quvir.sam > quvi ...
arrow pacbio basecallerversion assembly written 5 weeks ago by David_emir250 • updated 28 days ago by liu3yang0

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