User: misconstruction

Reputation:
20
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New User
Location:
European Union
Last seen:
1 year, 6 months ago
Joined:
4 years, 9 months ago
Email:
m************@gmail.com

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Posts by misconstruction

<prev • 6 results • page 1 of 1 • next >
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Get hg19 coordinates of SNPs from gwas catalog
... I have obtained a list of ~1000 SNPs from GWAS catalog, i.e: rs6856616 rs10947261 rs751728 rs2149085 rs11195128 rs11235667 rs9271366 For which I need the genomic position.  The GWAS catalog website states: "The SNP data in the ...
gwas catalog hg19 written 3.2 years ago by misconstruction20 • updated 13 months ago by Jack80
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Comment: C: edgeR: Correct pipeline for DE analysis with multiple conditions and batches
... Thanks for the response! I would like to directly use the names of conditions when doing the testing, rather than using an Intercept column and coef - how would you go about that? ...
written 3.5 years ago by misconstruction20
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Comment: C: edgeR: Correct pipeline for DE analysis with multiple conditions and batches
... I want to test all pairwise comparisons between conditions (no condition can be considered baseline'). I omitted the for-loop for clarity. ...
written 3.5 years ago by misconstruction20
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edgeR: Correct pipeline for DE analysis with multiple conditions and batches
... I'm using edgeR to test for DE genes in an expression matrix. For each sample if have a condition and a batch. I want to use the glm-functionality in edgeR to test for DE between conditions, while taking into account batches. Some example data to show my problem. Say if have a count matrix, EM,  of ...
R de edger rna-seq written 3.5 years ago by misconstruction20 • updated 3.5 years ago by Devon Ryan76k
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Calculate Ld Between All Pairs Of Snps, Both Within And Between Chromosomes
... Hi Biostar! After coming across a few papers claiming to find long range LD between SNPs on different chromosomes, I decided it would be fun to do this on my own dataset. The calculation itself is not terribly difficult, but a bit bothersome due to the huge RAM requirements. I have a an already f ...
genetics written 4.1 years ago by misconstruction20 • updated 4.1 years ago by chrchang5232.9k
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Small Problem: Multiple Alignment To Consensus Sequence
... Hi Biostar, I'm working with softclipped reads in python, mainly using biopython. I have gathered some small clusters of interesting sequences, which i want to do some motif analysis on, maybe blast them, etc. My problem is: i have between 3 and 20 sequences in each cluster, and i want to reduce ...
consensus python biopython multiple-alignment written 4.7 years ago by misconstruction20 • updated 4.7 years ago by k.nirmalraman900

Latest awards to misconstruction

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Calculate Ld Between All Pairs Of Snps, Both Within And Between Chromosomes
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Get hg19 coordinates of SNPs from gwas catalog
Popular Question 2.8 years ago, created a question with more than 1,000 views. For edgeR: Correct pipeline for DE analysis with multiple conditions and batches

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