User: cmcouto.silva

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Posts by cmcouto.silva

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Finding out assembly reference from bam file
... Yes, it did! My bad, sorry! I'm probably a little bit anxious. But all your tips were from great value! ...
written 8 weeks ago by cmcouto.silva30
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Comment: C: Finding out assembly reference from bam file
... Wow, I just got it! So, I must look if the chromosome size from my file matches the one from the reference assembly (by chromosome). I did it by looking at https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh37. Thanks!! ...
written 8 weeks ago by cmcouto.silva30
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Comment: C: Finding out assembly reference from bam file
... Sure! https://www.ebi.ac.uk/ena/data/view/PRJEB29074 ...
written 8 weeks ago by cmcouto.silva30
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Comment: C: Finding out assembly reference from bam file
... Yeah, I used this command, but there is no info regarding the assembly or reference used. ...
written 8 weeks ago by cmcouto.silva30
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Finding out assembly reference from bam file
... I am entirely newbie on WGS. At this point, I have worked just with data from SNP-array (plink format, .vcf, .haps/.sample), and I have to verify the allele frequency of a single SNP in WGS data. Therefore, I have to perform SNP calling, alright? The thing is, I did download the data in .bam forma ...
snp calling bam reference genome written 8 weeks ago by cmcouto.silva30 • updated 8 weeks ago by biobiu80
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Comment: C: How to interpret XPEHH (recent selection) score?
... So, about Giovanni's answer, his comment about -log(p-value) higher than 2 to be significant is correct? ...
written 6 months ago by cmcouto.silva30
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Comment: C: Fst between the combination of populations (pairwise)
... Glad to know that! Thanks for both of your answers! Best Regards, ...
written 8 months ago by cmcouto.silva30
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Fst between the combination of populations (pairwise)
... Hello everyone! I need to get Fst values for multiple populations combined pairwisely. __*For example:*__ ---------- **Populations:** Pop1 Pop2 Pop3 Pop4 Pop5 **Combinations:** Pop1 with Pop2 Pop1 with Pop3 Pop1 with Pop4 Pop1 with Pop5 Pop2 with Pop3 Pop2 with Pop4 ...
pairwise fst plink written 9 months ago by cmcouto.silva30 • updated 8 months ago by Biostar ♦♦ 20
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How to get a unique target gene for each SNP from different chromosomes/genes in a list at once?
... **Hello, folks!** I have a huge list with SNPs from different chromosomes/genes (human data set), and I wanna know the target genes for each one of them at once (if possible). It would be important to catch only one gene ID per SNP (top rated). ---------- **I have tried using the Ensembl Bioma ...
gene snp written 19 months ago by cmcouto.silva30 • updated 19 months ago by Alex Reynolds27k
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Comment: C: How to print the lines exclusively from unknown columns with missing(undef) valu
... Regarding to the original vcf file, I've observed that if I remove the hashtag "#" for any of the initial lines with comments or the header, csvtk points out that error. But only with the original one. After comparing with the filtered ones, I see the following: Original vcf file has 2356 tabs in t ...
written 2.1 years ago by cmcouto.silva30

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Supporter 8 months ago, voted at least 25 times.

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