User: CHANG

gravatar for CHANG
CHANG40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 year, 2 months ago
Joined:
6 years, 8 months ago
Email:
c*********@yahoo.com

about me

Posts by CHANG

<prev • 22 results • page 2 of 3 • next >
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workflow for combining multiple microarray studies of same platform
... I am pooling together tumor samples of of 4 different histology from 4 GEO studies that are done on Affymetrix U133 Plus 2.0. I want to compare differential genes and  between each tumor histology and blood.   Sample Tally   study tumor_histo_1 tumor_histo_2 tumor_histo_3 tumo ...
microarray written 5.2 years ago by CHANG40
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Which GRCh37 version to use from snpEff databases for BAMs mapped with GRCh37-lite?
... Does anyone know which version of GRCh37 to use from snpEff databases to annotate VCF files generated from BAMS mapped with GRCh37-lite. (https://browser.cghub.ucsc.edu/help/assemblies/) GRCh37-lite - This is a subset of the full GRCh37 human genome assembly (assembly accession GCA_000001405.1) ...
next-gen snp written 5.7 years ago by CHANG40 • updated 5.7 years ago by Pablo1.9k
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Comment: C: Absolute/Hapseg on Exome (WES) Data?
... https://github.com/aaronmck/CapSeg Have you tried this version of CapSeg by Aaron McKenna? ...
written 6.0 years ago by CHANG40
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Comment: C: Anyone Has A Working Example On How To Run BROAD's ABSOLUTE On Exome Sequencing
... Has anyone tried to this version of Capseg? https://github.com/aaronmck/CapSeg ...
written 6.0 years ago by CHANG40
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Comment: C: Anyone Has A Working Example On How To Run BROAD's ABSOLUTE On Exome Sequencing
... I ran varscan2 copycaller and bin results with dnacopy and sometimes it results in over 3000 segments, the default setting on absolute is 1500. Do you filter out some segments with low number of markers or merge the segments with varscan helper script mergeSegments.pl or simply increase the threshol ...
written 6.0 years ago by CHANG40
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Comment: C: Question About Mergesegment.Pl In Varscan 2
... this post might be helpful. 1. remove chromosome from your segmentation file that are not in your chr_arm length file. http://sourceforge.net/p/varscan/discussion/1073559/thread/996c2875/?limit=25#68b2 ...
written 6.0 years ago by CHANG40 • updated 13 months ago by _r_am31k
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Comment: C: Plotting Cnv Association And Gwas Association In A Single Plot
... I have a file with chr, start, end, log2ratio from segmented tumor/normal copy number data. I notice you script takes in chr, position, and value only, do you suggest I take the midpoint between start and end of each segments as "position" ? ...
written 6.0 years ago by CHANG40
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identifying miRNA in RNAseq
... I have Illumina hiseq pairend RNA sequencing on tumor samples. I am wondering if it is possible to identify microRNA expression in that data.   ...
rna-seq mirna written 6.2 years ago by CHANG40 • updated 6.2 years ago by Jelena Aleksic920
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Comment: C: RNA seq: tuxedo protocol - separate non-overlapping genes of same XLOC id in cuf
... There are more reads in ETHE1 than PHLDB3 , it doesn't seem like cufflink should merge them. I have attached a screen shot of igv ...
written 6.2 years ago by CHANG40 • updated 6.2 years ago by Devon Ryan97k
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RNA seq: tuxedo protocol - separate non-overlapping genes of same XLOC id in cuffdiff output
... I notice that there're two non-overlapping genes (PHLDB3, ETHE1) , but they have the same XLOC id = XLOC_018276 # cuffmerge's output - merged.gtf gene_id "XLOC_018276"; transcript_id "TCONS_00085241"; exon_number "16"; gene_name "PHLDB3"; oId "NM_198850"; nearest_ref "NM_198850"; class_code "="; t ...
rna-seq written 6.2 years ago by CHANG40

Latest awards to CHANG

Great Question 2.5 years ago, created a question with more than 5,000 views. For identifying miRNA in RNAseq
Popular Question 2.5 years ago, created a question with more than 1,000 views. For TCGA RNAseqV2 upper quartile normalization with x1000 adjustment factor
Popular Question 2.5 years ago, created a question with more than 1,000 views. For TCGA RNAseqV2 upper quartile normalization with x1000 adjustment factor
Popular Question 3.6 years ago, created a question with more than 1,000 views. For TCGA RNAseqV2 upper quartile normalization with x1000 adjustment factor
Popular Question 4.0 years ago, created a question with more than 1,000 views. For identifying miRNA in RNAseq
Popular Question 4.8 years ago, created a question with more than 1,000 views. For identifying miRNA in RNAseq
Popular Question 4.8 years ago, created a question with more than 1,000 views. For identifying miRNA in RNAseq

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