User: bounlu

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bounlu130
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Singapore
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1 month, 2 weeks ago
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5 years, 5 months ago
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Posts by bounlu

<prev • 33 results • page 1 of 4 • next >
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Comment: C: How To Convert Gencode Gtf Into Bed Format ?
... gtf2bed from bedops do not work for GENCODE comprehensive gtf file if there are features without transcript ID in the attributes: convert2bed -i gtf < gencode.v27lift37.annotation.gtf > gencode.v27lift37.annotation.bed Error: Potentially missing gene or transcript ID from GTF attr ...
written 8 weeks ago by bounlu130
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Answer: A: Training dataset for NGS HLA typing (reads >200bp from PCR amplicons)
... The references to HLA typing tools might help as they usually train their software on public datasets: https://www.nature.com/articles/jhg2015102/tables/2 ...
written 3 months ago by bounlu130
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Answer: A: Software For Hla Typing Using Ngs?
... Here is a compiled list in a paper: https://www.nature.com/articles/jhg2015102/tables/2 ...
written 3 months ago by bounlu130
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Answer: A: how to extract sample id with bcftools or vcftools
... alternatively you can use vcftools: vcf-query -l input.vcf ...
written 3 months ago by bounlu130
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Comment: C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
... Trimmomatic beats up conventional trimming tools. ...
written 4 months ago by bounlu130
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Comment: C: Script for analyzing idat (illumina) microarray files with limma, any suggestion
... I tried but gave up since the debugging takes longer than creating my own script. Some errors below: > > topTable = beadAnalyze(idats = c("9533701097_A_Grn.idat","9533701097_B_Grn.idat","9533701097_C_Grn.idat","9533701097_D_Grn.idat"),names > = c("H7_2a_2v_A","H7_2a_2v_B","H7_2v_C","H7_2v_ ...
written 5 months ago by bounlu130
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Comment: C: Script for analyzing idat (illumina) microarray files with limma, any suggestion
... Can you please update the link? Thanks. ...
written 5 months ago by bounlu130
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Comment: C: How To Download All Sra Samples At Once ?
... How to do this in R for controlled access data hosted at dbGaP if we have the key file rather than using prefetch/fastq-dump? ...
written 9 months ago by bounlu130
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Comment: C: Extract Sequence From Fasta File Using Ids From A Separate File
... you can install it via anaconda: `conda install ucsc-fasomerecords` ...
written 13 months ago by bounlu130
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Comment: C: FastQ quality check : what can we correct ?
... Currently the newest version is 0.11.5 although there are no new metrics on top of yours. ...
written 18 months ago by bounlu130

Latest awards to bounlu

Popular Question 9 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to get the coding sequence of each isoform of a gene?
Popular Question 12 months ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Popular Question 13 months ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Supporter 20 months ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA

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