User: khatami.mahshid

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Posts by khatami.mahshid

<prev • 27 results • page 1 of 3 • next >
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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 8 weeks ago by khatami.mahshid10 • updated 8 weeks ago by zx87548.4k
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Comment: C: Neandertals VCF file
... yes they are. both refrence.fa and bam files are hg19. ...
written 8 weeks ago by khatami.mahshid10
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Comment: C: Neandertals VCF file
... the refrence.fa is a hg19 human genome fasta file I download from UCSC. ...
written 8 weeks ago by khatami.mahshid10
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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 8 weeks ago by khatami.mahshid10 • updated 8 weeks ago by Pierre Lindenbaum124k
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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 8 weeks ago by khatami.mahshid10 • updated 8 weeks ago by WouterDeCoster42k
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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 8 weeks ago by khatami.mahshid10
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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 8 weeks ago by khatami.mahshid10 • updated 8 weeks ago by zx87548.4k
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Diffrence between 2 VCF files
... Hi all, I found VCF file for Denisova in UCSC genome browser in [this link.][1] but there is a paragraph in explanation of UCSC that introduce a new link for Denisova, [this is the link.][2] the paragraph is this: > Comprehensive VCF files that include information for > homozygous-reference ...
snp written 9 weeks ago by khatami.mahshid10 • updated 27 days ago by Biostar ♦♦ 20
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Comment: C: Generating Both Pileup And Vcf/Bcf Using Samtools Mpileup
... where can i download it? I want to map with human genome hg19? ...
written 9 weeks ago by khatami.mahshid10
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Comment: C: Generating Both Pileup And Vcf/Bcf Using Samtools Mpileup
... what is reference.fa file? where can I download it? ...
written 9 weeks ago by khatami.mahshid10

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