User: khatami.mahshid

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Posts by khatami.mahshid

<prev • 30 results • page 1 of 3 • next >
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Comment: C: how to find haplotype of SNPs
... I have 3 SNPs and 450 samples. my problem is more about what "0/1" should be considered? I know it is ref/alt but I got confused that which one is in haplotype? ref or alt? ...
written 5 weeks ago by khatami.mahshid20
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how to find haplotype of SNPs
... Hi all, I have these format of SNPs: "0/0" "0/1" "1/1" I know the ref/alt alleles. for these SNPs and for specific donors how can I find out haplotypes? for example, if my donors were like these : ---------------------------- donor1: SNP1 - SNP2 - SNP3 0/0 - 0/1 - 0/0 ...
snp written 5 weeks ago by khatami.mahshid20 • updated 5 weeks ago by colindaven2.1k
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biocircossnptrack function in biocircos library
... Hi, I run the following code and get the plot attached. my question is why all points are located at the left edge of tracks. why they don't spread in tracks? tracklist = BioCircosSNPTrack('mySNPTrack', points_chromosomes, points_coordinates, points_values, color ...
R snp written 9 weeks ago by khatami.mahshid20
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Merge bam files
... I already ask a question about this, but I didn't get my answer complete. https://www.biostars.org/p/399693/ I have 6 bam file that one of them is just 2 Mb and one is 2 Gb. I think the comparison between VCF file of these bam files is not fair, because they don't have equal read. so I want to mer ...
vcf bam samtools snp written 6 months ago by khatami.mahshid20 • updated 6 months ago by zx87549.1k
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Comment: C: Neandertals VCF file
... yes they are. both refrence.fa and bam files are hg19. ...
written 6 months ago by khatami.mahshid20
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Comment: C: Neandertals VCF file
... the refrence.fa is a hg19 human genome fasta file I download from UCSC. ...
written 6 months ago by khatami.mahshid20
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Neandertals VCF file
... Hi all, I have Bam files of Neandertals from UCSC database. I tried to convert these bam files to VCF files with `samtools mpileup` and `bcftools mpileup` . but what I received is like these : chr10 298350 . C <*> 0 . DP=1 PL 0,3,22 chr10 298351 . A <*> 0 . DP=1 PL 0,3,20 chr10 30603 ...
snp written 6 months ago by khatami.mahshid20 • updated 6 months ago by Pierre Lindenbaum127k
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@RG ( read group ) in neandertals
... I have some bam files from Neandertals I downloaded from UCSC. I want to first merge them and then convert to VCF file. but when I search for @RG in bam files to see if they are from the same library, it shows they don't have @RG. I use this command to find @RG in bam files: samtools view -H SL ...
rna-seq snp written 6 months ago by khatami.mahshid20 • updated 6 months ago by WouterDeCoster43k
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Comment: C: merge Bam files and get VCF file
... I have read the link you shared, I didn't understand it properly. how should my bam file header be to use the second approach? ...
written 6 months ago by khatami.mahshid20
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Merge bam files and get VCF file
... I have 2 sorted Bam files and I want to merge them and get a VCF file from them using samtools pileup. first i merge these 2 files with `samtools merge` and then I get a VCF file as output. samtools mpileup genome.fa merged-bam.bam output.vcf then I use samtools mpileup genome.fa 1.ba ...
bam rna-seq snp written 6 months ago by khatami.mahshid20 • updated 6 months ago by zx87549.1k

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