User: sonia.olaechea

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Posts by sonia.olaechea

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Comment: C: align specific region of human to panTro6
... And another question @JC : I have done the lift over and I'm having a look at the sequences with `UGene` (similar to `Bioedit`). I see now that a big part of panTro6 sequence is displaced just by 1 or 2 nucleotides in some regions. My next step will be to calculate the divergence between both specie ...
written 12 days ago by sonia.olaechea100
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Comment: C: align specific region of human to panTro6
... I would like to eliminate from my human fasta those positions that don't have a match with the panTro fasta. ...
written 12 days ago by sonia.olaechea100
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Comment: C: align specific region of human to panTro6
... Okey! I hadn't heard about LiftOver, but that's exactly what I need! Thank you so much! ...
written 12 days ago by sonia.olaechea100
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align specific region of human to panTro6
... Hi everyone! I'm trying to efficiently align a fasta file with a human sequence to panTro6 sequence but I'm not sure on how to avoid the gaps between both species. Are there tools that take these gaps already into account? Thanks in advance for the help! ...
pantro6 alignment written 13 days ago by sonia.olaechea100 • updated 13 days ago by JC9.7k
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Comment: C: twoBitToFa retrieving longer sequence than expected in hg19
... Thanks to both of you, you were both right!! It turns out that my `bash command` was counting both the `N's` and the header line of the sequence!! ...
written 16 days ago by sonia.olaechea100
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twoBitToFa retrieving longer sequence than expected in hg19
... Hi all! I'm using twoBitToFa to retrieve a specific region of a chromosome in hg19. The command I'm using is: twoBitToFa http://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit myfile.fa -seq=chr1 -start=891021 -end=125030866 I would expect there to be 125030866 - 891021 = 124139845 nucleotides. ...
twobittofa hg19 written 18 days ago by sonia.olaechea100 • updated 18 days ago by wm350
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Comment: C: Converting ms or msms output to PLINK or VCF files
... Hello! I'm facing the same issue as well... I've tried to use `ms2geno` but haven't managed to make it work properly. Has anyone found a better option? ...
written 27 days ago by sonia.olaechea100
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Comment: C: gene ontology with reference list
... The output of both commands is the same: 17647 genes... Thank you anyway ;) ...
written 5 months ago by sonia.olaechea100
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Comment: C: gene ontology with reference list
... I used webtool Gene Ontology (GO):http://geneontology.org/ I only pasted my list on the webpage and it redirects me to PANTHER, where I can add my reference gene list. At this point it tells me that I have duplicate genes in my reference list... ...
written 5 months ago by sonia.olaechea100
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gene ontology with reference list
... Hi all, I would like to do an enrichment analysis/gene ontology analysis after an RNAseq differential expression analysis. For this, I would like to use a set of reference genes. I have already tried GO, but it's giving me some errors (it says that I have duplicate genes, while I've checked and I d ...
gene ontology rna-seq written 5 months ago by sonia.olaechea100 • updated 5 months ago by O'kin-110

Latest awards to sonia.olaechea

Popular Question 7 months ago, created a question with more than 1,000 views. For 1000Genomes population allele frequencies for list of SNPs
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Popular Question 9 months ago, created a question with more than 1,000 views. For vcftools --TajimaD in sliding windows

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