User: bxia

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bxia120
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Posts by bxia

<prev • 102 results • page 1 of 11 • next >
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edgeR 2GB table
... I have a table with 10000 htseq samples...the file size is 1.7Gb... how to analyze it with edgeR? ...
rna-seq written 13 hours ago by bxia120
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Comment: C: how to convert SGD standard name to SGD systematic ID?
... Yes, for example, I have a gene name, **RPL7B**, which I can find the SGD systematic id by search in there website as **YPL198W** But I can't find a file containing theses two kinds of IDs in downloads section of SGD. Have anyone known the table download info in SGD database? Thanks, ...
written 7 weeks ago by bxia120
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how to convert SGD standard name to SGD systematic ID?
... does SGD have a table to map theses two names? I didn't find one in their download database.. ...
sgd written 7 weeks ago by bxia120
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How does WGS normalization perform between samples
... I am currently using whole genome sequencing to identify structure variation (SV) I wonder whether I need to perform normalization between the samples. For example, 2-micron 10 1 N . . SVTYPE=DUP;STRANDS=-+:155;SVLEN=6307;END=6317;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;SU=155;PE=0;SR=155 G ...
whole genome sequencing written 8 weeks ago by bxia120
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Comment: C: LUMPY SV call without quality score
... Thanks for your explanation. I have read the VCF format description, I thought it will tell me the details of the changes.. ...
written 9 weeks ago by bxia120
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Comment: C: LUMPY SV call without quality score
... But the other problem I have is the REF column are all N, although it tells me it is DEL or INDEL or something else.. ...
written 9 weeks ago by bxia120
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Comment: C: LUMPY SV call without quality score
... I checked the other people's post, they have it and all the REF column are shown as N.. ...
written 9 weeks ago by bxia120
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LUMPY SV call without quality score
... I am using LUMPY to call structure variation, but the problem is all the quality score returned by LUMPY is marked as '.' Is it due to low sequencing depth? ...
wgs written 9 weeks ago by bxia120
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cpath is not available for cytoscape?
... I am following the cytoscape protocol from nature paper. However, I can't find cpath plugins in cytoscape app store anymore. Is it being disabled? For human protein interaction, is there other types of apps could do the same thing? Thanks, ...
protein interaction written 12 weeks ago by bxia120 • updated 11 weeks ago by cannin230
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Comment: C: How Gro-seq identify enhancer RNA?
... Hi, Kevin, I understand that the GRO-seq identify the location for the nascent RNA. Although enhancer is not restricted to TSS, most of them overlap with TSS. In addition, the signal i see on the genebody belong to enhancer RNA or mRNA? Thanks, ...
written 5 months ago by bxia120

Latest awards to bxia

Popular Question 28 days ago, created a question with more than 1,000 views. For FastQC after read sequences, nothing happened...
Popular Question 4 weeks ago, created a question with more than 1,000 views. For FastQC after read sequences, nothing happened...
Centurion 7 weeks ago, created 100 posts.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For FastQC after read sequences, nothing happened...
Popular Question 12 weeks ago, created a question with more than 1,000 views. For FastQC after read sequences, nothing happened...
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Interpretation of TCGA clinical data
Popular Question 5 months ago, created a question with more than 1,000 views. For which annotation I should for RNA-seq? Ensembl, UCSC or refseq?
Popular Question 5 months ago, created a question with more than 1,000 views. For HTSEQ count is the raw count, not RPKM or FPKM, right?
Popular Question 5 months ago, created a question with more than 1,000 views. For how do I know the breast cancer subtype based on TCGA clinical data
Popular Question 10 months ago, created a question with more than 1,000 views. For how do I know the breast cancer subtype based on TCGA clinical data
Popular Question 14 months ago, created a question with more than 1,000 views. For how do I know the breast cancer subtype based on TCGA clinical data
Student 17 months ago, asked a question with at least 3 up-votes. For HTSEQ count is the raw count, not RPKM or FPKM, right?
Supporter 18 months ago, voted at least 25 times.

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