User: hafiz.talhamalik

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New User
Location:
Pakistan
Last seen:
2 days, 15 hours ago
Joined:
3 years ago
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h***************@gmail.com

Posts by hafiz.talhamalik

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Extracting miRNA data from RNA-Seq data set
... Ok thanks got it...! ...
written 8 days ago by hafiz.talhamalik30
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Extracting miRNA data from RNA-Seq data set
... Can i extract miRNA data from RNA-Seq data set ? and if possible, can i extract deferentially expressed microRNA's from it ? ...
rna-seq mirna written 8 days ago by hafiz.talhamalik30
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Comment: C: How to compulate the FPKM of differentially expressed transcripts (DETs)
... to differentiate between RPKM/FPKM see this video. its quite helpful https://www.youtube.com/watch?v=TTUrtCY2k-w ...
written 8 days ago by hafiz.talhamalik30
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Answer: A: How to compulate the FPKM of differentially expressed transcripts (DETs)
... You calculate RPKM/FPKM using simple three steps. 1-Count up the total reads in a sample and divide that number by 1,000,000 – this is our “per million” scaling factor. 2-Divide the read counts by the “per million” scaling factor. This normalizes for sequencing depth, giving you reads/fragments per ...
written 8 days ago by hafiz.talhamalik30
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Comment: C: Standard Practice of making VCF file from SAM file
... okz. that helped. Thanks alot ...
written 12 days ago by hafiz.talhamalik30
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Comment: C: Standard Practice of making VCF file from SAM file
... oh okz. I used samtools/bcftools pipeline. I made a vcf file too but i wanted to counter check that with GATK pipeline. one more thing I have a genome of around mb, and samtools pipeline gave me a vcf file with around 2300 variants. Is it normal ? or did I made a mistake ? ...
written 13 days ago by hafiz.talhamalik30
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Comment: C: Standard Practice of making VCF file from SAM file
... I am trying to follow this one. But BaseRecalibration requires input of -knownSites latest_dbsnp.vcf. and i have whole genome of bacteria so what should i do with this parameter ? and what about next step ? ...
written 13 days ago by hafiz.talhamalik30
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Comment: C: Standard Practice of making VCF file from SAM file
... I have used PICARD for SortSam, and MarkDuplicates. Now which one to use next ? ...
written 13 days ago by hafiz.talhamalik30
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Standard Practice of making VCF file from SAM file
... Can any one guide me to about what standard GATK tools to use when making a vcf file from allignment sam file ? I'm kinda stuck. confused which one to use and when. ??? ...
gatk snp written 13 days ago by hafiz.talhamalik30 • updated 6 days ago by Biostar ♦♦ 20
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Understanding output of GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification tool
... I am trying to find ROH using GARLIC tool. Szpiech, Z. A., Blant, A., & Pemberton, T. J. (2017). GARLIC: genomic Autozygosity regions likelihood-based inference and classification. Bioinformatics, 33(13), 2059-2062. my output is shown below. i am not sure about result and also m not been able to ...
roh population genomics genomics written 9 weeks ago by hafiz.talhamalik30

Latest awards to hafiz.talhamalik

Popular Question 5 months ago, created a question with more than 1,000 views. For Threshold of removing genes with low counts ?
Popular Question 5 months ago, created a question with more than 1,000 views. For Which package to use for RPKM/FPKM RNA-seq counts?

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