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User: seta

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seta • 1.2k
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Posts by seta

<prev • 739 results • page 1 of 74 • next >
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Window-based Fst analysis
... Hi all, I used vcftools for Fst calculation of a set of snp (about 2000) with varying window size and step, like window and step size of 50bp-5bp, 500bp-50bp, 1000bp-100bp, and 100kbp-10kbp. Obviously, the calculated Fst is different among different parameters. But, I'm not sure how I should select ...
population genetic fst written 1 day ago by seta • 1.2k
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Comment: C: bedtools closest return no output!
... Thanks, the files have not such a problem that you mentioned. I tried `bedtools window` and worked well. Sorry, what's the main difference between these two options, closest and window? ...
written 4 days ago by seta • 1.2k
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bedtools closest return no output!
... Dear all, I'm trying to get the upstream and downstream genes of a specific long non-coding RNA (lncRNA) in rat. To this end, I download the rat GTF file from Ensembl and converted to bed format by `fgrep -w gene rat.gtf | sed 's/[";]//g;' | awk '{OFS="\t"; print $1, $3, $4-4,$5,$12,0,$7,$18,$14,$1 ...
bedtools gtf nearest gene written 4 days ago by seta • 1.2k
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Comment: C: Convert HLA allele to Genepop format
... yes, I can use it. But, I just want to make sure this conversion is right? ...
written 9 days ago by seta • 1.2k
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Comment: C: Convert HLA allele to Genepop format
... Yes Kevin, I saw those links, I tried the PGDspider, but it didn't work for me. Based on the example of genepop format at [here][1], I manually changed the above format (in the original post) to the below format: Loc1, Loc2, Loc3, Loc4, Loc5 POP NA18500, 3301 7401 5801 7801 1601 NA ...
written 9 days ago by seta • 1.2k
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Comment: C: Recoding HLA Alleles by 01
... Hi Kevin, what about the conversion of HLA allele to popgene format; could you please take a look at [this post ][1]? do you have any suggestion? Thanks [1]: https://www.biostars.org/p/389549/ ...
written 9 days ago by seta • 1.2k
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Convert HLA allele to Genepop format
... Dear all, I'm trying to used PGDspider tool to convert HLA allele file to Genepop format, however I'm not successful with it. I selected "convert" in file format (input), and "Genepop" for output format. Could you please let me know your way to convert HLA allele to Genepop format or any format acc ...
genepop format convert pgdspider written 9 days ago by seta • 1.2k
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Comment: C: Calculating Fst from simulations
... Hi Rubal, It's so late; however, could you please tell me how you solve the problem? ...
written 10 days ago by seta • 1.2k
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Comment: C: Picking random SNPs from 1000 Genomes using Vcftools
... Sorry, which answer do you mean? please kindly let me know if you have any suggestions. ...
written 16 days ago by seta • 1.2k
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Comment: C: Unexpected outcome: Gene Enrichment using Fisher's Test
... Hi Michael, I used the similar fisher test on SNPs (2400 SNPs), but when I calculated OR with fisher test, there are multiple SNPs with OR < 1 while "alternative=greater" was used in the fisher test command; so I expected all enriched SNP (OR > 1). Could you please let me know what's happene ...
written 20 days ago by seta • 1.2k

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Great Question 6 days ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
Popular Question 14 days ago, created a question with more than 1,000 views. For rRNA contamination in poly A-enriched libraries
Great Question 5 weeks ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
Great Question 8 weeks ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For rRNA contamination in poly A-enriched libraries
Scholar 9 weeks ago, created an answer that has been accepted. For A: get chromosomal location of housekeeping genes
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: hello i know i must accept that im a stupid
Popular Question 10 weeks ago, created a question with more than 1,000 views. For rRNA contamination in poly A-enriched libraries
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Popular Question 4 months ago, created a question with more than 1,000 views. For rRNA contamination in poly A-enriched libraries
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Great Question 4 months ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
Popular Question 5 months ago, created a question with more than 1,000 views. For ID conversion by BioMart
Great Question 5 months ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
Great Question 5 months ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
Great Question 5 months ago, created a question with more than 5,000 views. For How to get length of selected contigs within a fasta file generated by transcriptome assembly?
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