User: khatami.mahshid

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Posts by khatami.mahshid

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Geuvadis Normalization method
... I'm not sure , are you sure about this? ...
written 11 days ago by khatami.mahshid20
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Geuvadis Normalization method
... Hi I am using the GEUVADIS dataset, in the readme of the project I found this paragraph talking about normalization: > Normalization: None: raw read counts Library depth: Read counts scaled by total number of mapped reads (mRNA), or total number reads mapping to miRNAs (miRNA) per sample, t ...
snp rna-seq written 11 days ago by khatami.mahshid20
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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 8 months 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 8 months ago by khatami.mahshid20 • updated 8 months ago by colindaven2.4k
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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 months 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 13 months ago by khatami.mahshid20 • updated 13 months ago by zx87549.7k
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Comment: C: Neandertals VCF file
... yes they are. both refrence.fa and bam files are hg19. ...
written 13 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 13 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 13 months ago by khatami.mahshid20 • updated 13 months ago by Pierre Lindenbaum131k
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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 13 months ago by khatami.mahshid20 • updated 13 months ago by WouterDeCoster44k

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Supporter 13 months ago, voted at least 25 times.

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