User: nataliagru1

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nataliagru150
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Posts by nataliagru1

<prev • 29 results • page 2 of 3 • next >
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BLASTn output format start position larger than stop position
... Dear Community, I am currently running an experiment to identify gene expansion in parasite genomes. I have collected respected gene sequences and created a blast database of my parasite reference genomes using blast db function. I use blastn and search against my parasite reference genome with m ...
blastn output blast outfmt 6 blast blastn written 4 months ago by nataliagru150 • updated 4 months ago by Sej Modha4.7k
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Comment: C: Remove sequences with (50% gaps) from MSA
... Thank you very kindly for your response!! Very helpful indeed! I had some computer issues and am now re-installing biopython and other programs! Will test your code and report back once I have everything up and running! Greatly appreciate you taking the time! ...
written 4 months ago by nataliagru150
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Comment: C: Remove sequences with (50% gaps) from MSA
... Thank you for your response. Yes, I first did remove columns that had a majority position in gaps with trimAL. It's the later I am having an issue with. I am uncertain of trimAL parameters to remove undesirable sequences and was, therefore, wondering if there was a simple way to write a script to re ...
written 5 months ago by nataliagru150
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Remove sequences with (50% gaps) from MSA
... How do I remove sequences from my MSA that contain 50% gaps? I know there are various posts about removing columns with gaps. But I'm looking for a simple script to identify alignments within my MSA that have >50% gaps "-" and remove them. I am not well versed in BioPython AlignIO. I feel as thou ...
alignment multple sequence alignment sequence msa written 5 months ago by nataliagru150 • updated 5 months ago by Mensur Dlakic6.5k
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Comment: C: Vcftools Runs Of Homozygosity Option
... Hello! I too am running into the same issue! Can anyone explain this?!! Thank you! ...
written 13 months ago by nataliagru150
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Answer: A: PopGenome software: concatenating chromosomes and coalescent simulations
... Dear All, popgenome actually has an option to concatenate genome classes. Therefore you can put each chromosome into a class (genome_chr1.class, genome_chr2.class, genome_chr3.class, etc.) and merge all genome classes via concatenate.classes(genome_chr1.class, genome_chr2.class, genome_chr3.class). ...
written 13 months ago by nataliagru150 • updated 10 months ago by RamRS30k
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Is it acceptable to use ShapeIT for parasite genomes?
... Dear all, I am posting this question to BioStars community as I am trying to get a consensus on phasing softwares such as ShapeIT and IMPUTE2, Beagle etc. and their use and application on parasites genomic data (species that are diploid). For a recent experiment I wanted to use fineStructure to c ...
shapeit impute2 haplotype phasing beagle written 13 months ago by nataliagru150 • updated 6 months ago by Biostar ♦♦ 20
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Answer: A: formating for fineSTRUCTURE input
... Hello. You need to use a program such as ShapeIT or IMPUTE2 to phase your VCF file. ShapeIT takes VCF files as input and will output a phased file format which you will need to convert to chrompainter format (these scripts and tools are provided on fineStructure website). In addition everything I am ...
written 14 months ago by nataliagru150
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Answer: A: Generating genetic map file to use as input for shapeit
... It is actually rather challenging to produce a genetic map file from scratch. ShapeIT does have the option to exclude the genetic map and use a function --roh or "recombination rate". This is simply one value. You should be able to find a recombination rate value in scientific literature for the spe ...
written 14 months ago by nataliagru150
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Comment: C: PopGenome tutorial files
... Indeed I have attempted to contact them many times to no avail! ...
written 14 months ago by nataliagru150

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