User: bounlu

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bounlu140
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Posts by bounlu

<prev • 38 results • page 1 of 4 • next >
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Answer: A: Splicing factor database
... none of the above links work. any other suggestions? ...
written 10 weeks ago by bounlu140
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Comment: C: Find 12-mer not mapping to the human genome
... Both comments are very useful. I generated all possible 12-mers in R: x = expand.grid(rep(list(c("A", "C", "T", "G")), 12)) write.delim(x, file = "12-mers_all_combinations.txt", col.names = F) I was thinking to "map" them to the reference genome with BLAT and pick the unmapped ones, but fr ...
written 11 weeks ago by bounlu140
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Find 12-mer not mapping to the human genome
... Hi, I would like to find 12-mer short DNA sequences which do not map to the human genome and do not form self-mer as well. I want them to be as unique as possible. How can I get them? Which tool/software should I use? ...
alignment sequence mapping sequencing written 11 weeks ago by bounlu140 • updated 11 weeks ago by 5heikki7.8k
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circRNA-Seq analysis tools
... Hello, I have circRNA-Seq samples and I am looking for tools to identify the circRNAs in these samples. In circRNA-Seq, all linear form of RNAs are degraded to enrich the circRNAs, which is still in principle RNA-Seq. There are plenty of tools to detect circRNAs from RNA-Seq data such as [CIRCexp ...
circrna-seq circrna written 3 months ago by bounlu140 • updated 11 weeks ago by IP500
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Comment: C: VCF files: Change Chromosome Notation
... Or the goddesses will decide to keep "chr"s in all datasets and we can live in peace too (or this could be the cause of another war again?) ...
written 3 months ago by bounlu140
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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 7 months ago by bounlu140
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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 8 months ago by bounlu140
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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 8 months ago by bounlu140
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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 8 months ago by bounlu140
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Comment: C: Bwa Mem Method For Mapping, With Or Without Trimming Reads?
... Trimmomatic beats up conventional trimming tools. ...
written 9 months ago by bounlu140

Latest awards to bounlu

Popular Question 14 months ago, created a question with more than 1,000 views. For How to identify non-expressed genes in microarray?
Popular Question 15 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 17 months ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Popular Question 18 months ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA
Supporter 2.1 years ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Homozygous/Heterozygous Deletions (Copy Number Variation) in TCGA

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