User: bounlu
bounlu • 170
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Posts by bounlu
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Comment:
C: Getting error in running rMATS
... @Kevin rocks, as usual ! ...
written 6 weeks ago by
bounlu • 170
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Answer:
A: Splicing factor database
... none of the above links work. any other suggestions? ...
written 4 months ago by
bounlu • 170
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... 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 4 months ago by
bounlu • 170
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... 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? ...
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... 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 ...
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... 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 5 months ago by
bounlu • 170
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... 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 9 months ago by
bounlu • 170
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... 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 10 months ago by
bounlu • 170
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... Here is a compiled list in a paper:
https://www.nature.com/articles/jhg2015102/tables/2 ...
written 10 months ago by
bounlu • 170
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... Alternatively you can use *vcftools*:
vcf-query -l input.vcf ...
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