User: shinken123

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shinken12360
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Posts by shinken123

<prev • 37 results • page 1 of 4 • next >
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Hapmap to vcf
... Hi all, I have a hapmap file from tassel and I want to convert it to a vcf. Tassel can convert the file but takes the major allele as the reference and the minor as the alternative. I want to use the reference genome for the reference alleles and set the alleles different from the reference genom ...
vcf hapmap convert written 4 weeks ago by shinken12360 • updated 4 weeks ago by RamRS18k
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Calculation of heterozygosity
... Hi everyone, I am calculating the proportion of heterozygous loci per individual using the next simple formula: number of heterozygous loci/number of genotyped loci I am using SNPs calls from illumina data and my values are close to 0.5. However these lines are supposed to be maize homozygou ...
genome next-gen sequencing written 3 months ago by shinken12360
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Perform of disco Snp with low coverage samples
... Hi All, I have some hundreds of pair end illumina fastq files with really low coverage 0.5x (Skim Seq). I am wondering if discoSNP could make a decent work calling SNPs from these samples. Or which software you recommend me? Would be good to be able to call SNPs using even a single read. Because ...
discosnp snp calling low coverage written 4 months ago by shinken12360 • updated 4 months ago by pierre.peterlongo830
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Comment: C: trying to reproduce mirbase blastn
... For some reason that doesn't work. ...
written 7 months ago by shinken12360
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trying to reproduce mirbase blastn
... Hi I am trying to reproduce blastn results from the mirbase webpage. Using this: blastn -query query -db db -max_target_seqs 100 -reward 5 -penalty -4 -num_threads 8 -word_size 4 -evalue 10 -outfmt "6 qseqid sseqid positive evalue" and blastn -query query -db db -task blastn-short -m ...
mirbase blastn written 7 months ago by shinken12360
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Ontology gramene releases
... Dear all, I am looking for a maize ontology gramene .ga file for maize. The only one that I can found is [here](ftp://ftp.gramene.org/pub/gramene/release-55/ontology/go/]) However is for release 55, and it looks that this release is for maize genome V4. If I want the .ga file for B73 RefGen_v3 w ...
gene assembly written 12 months ago by shinken12360
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bcftools consensus trying to apply the alternative allele if my sample is homozygous or heterozygous alternative for the site
... Hi all I am using bcftools consensus to add the alternative SNPs to a fasta file. I am running it in two ways: bcftools consensus -i -s sample1 -f reference.fasta file.vcf.gz > pseudoreference.fasta bcftools consensus -H A -s sample1 -f reference.fasta file.vcf.gz > pseudoreference ...
sequence snp written 13 months ago by shinken12360
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Answer: A: Obtaining the top matches from blast
... Using the output of blast using the option -outfmt 6 What about: awk '!seen[$1]++' Blast_output_file.txt > Besthit_Blast_output_file.txt ...
written 14 months ago by shinken12360
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obtain reference and base from read in a region from a bam file
... Hi I want to obtain the reference base and the base of the reads that align in a certain region from a bam file. And get something like this: Reference Read1 Read2 A A indel or mismatch C G ...
alignment written 19 months ago by shinken12360 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: A: GBS SNPs calling
... Thank you, the paper was really helpful. ...
written 20 months ago by shinken12360

Latest awards to shinken123

Popular Question 4 weeks ago, created a question with more than 1,000 views. For GBS SNPs calling
Popular Question 11 weeks ago, created a question with more than 1,000 views. For vcf-merge is giving me a few SNPs in the merged vcf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Obtaining the top matches from blast

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