User: Wilber0x

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Wilber0x10
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Posts by Wilber0x

<prev • 8 results • page 1 of 1 • next >
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RAxML generate best tree from 500 bootstrap trees
... I am using RAxML. I want to make a single maximum likelihood tree based on 500 boostraps. I am also using partitions for my alignment. I used this command in RAxML: raxmlHPC-PTHREADS-AVX2 -m GTRGAMMA -p $RANDOM -x $RANDOM -N 500 -T 4 -s myAlignment.phy -q partitionSchemel.txt -n output.tre I ...
sequence phylogenetics raxml written 6 weeks ago by Wilber0x10 • updated 6 weeks ago by ugurcabuk130
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alignment of multiple multifasta files- MAFFT command line
... I have a folder with around 100 multifasta files. I want to align each multifasta file inidividually using MAFFT. Each multifasta file ends with `.unaligned.fasta` I would like to change those file endings to `aligned.fasta`. I have tried using MAFFT normally on the command line as so, with asteris ...
alignment sequence mafft written 8 months ago by Wilber0x10 • updated 8 months ago by h.mon30k
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HMMER installed with conda: no tutorial folder
... I am trying to use HMMER for the first time. I installed it as per instructions in the user guide, using anaconda: conda install -c bioconda hmmer However, now I want to run through the tutorial, and there is no tutorial directory in the HMMER directory installed. There are 9 directories or su ...
genome installation alignment hmmer written 9 months ago by Wilber0x10 • updated 9 months ago by konkelzach10
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truncate VCF files so they are same length
... I have five VCF files, for five different species. They were all aligned to the same reference sequence. Some VCF files are longer than others, as more sequence aligned to the reference sequence in different species. The different chromosomes also have different numbers of variants for each species. ...
vcf genome sequence snp written 9 months ago by Wilber0x10 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: finding specific SNPs in VCF files
... Thank you. SNPs from organism A are also in a vcf file. ...
written 12 months ago by Wilber0x10
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finding specific SNPs in VCF files
... I have a list of SNPs from one organism (organism A). I have genome skims of hybrids between organism A and other species. What methods can I use to see if SNPs from organism A are present in the hybrids? I have used bowtie2 to map genome skims to the same reference I used when finding SNPs for or ...
gene genome next-gen snp alignment written 12 months ago by Wilber0x10 • updated 12 months ago by Brice Sarver3.5k
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Decrease stringency of bowtie2
... I want to decrease the stringency of bowtie2 when mapping. How can I increase the overall alignment rate? My index is from one of two closely related organisms (species A). I want to find the sweet spot where my reads from species A align to the index at a very high rate, but reads from species B d ...
assembly next-gen sequence alignment written 12 months ago by Wilber0x10 • updated 12 months ago by h.mon30k
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Identifying unique SNPs between species
... I have 8 samples each with a VCF file made from aligning a genome skim of that sample to the same reference. I can see the number of SNPs for each sample in their individual VCF files, but I want to know how many SNPs and which SNPs are unique to each sample. Can I merge the VCF files into one to ...
vcf alignment snp written 13 months ago by Wilber0x10 • updated 13 months ago by finswimmer13k

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