User: ammarsabir15

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ammarsabir1560
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Posts by ammarsabir15

<prev • 75 results • page 1 of 8 • next >
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No Prominent Change in Structure of Mutated Proteins
... I am working on Parkinson disease causing protein **PINK1**, I am focusing on **26 disease causing variants** for parkinson. These variants are reported [here][1]. There is no PDB structure for PINK1, thus I predicted it using **I-Tasser**. I used this structure for homology modelling through mode ...
alignment sequence protein-modelling written 2.2 years ago by ammarsabir1560 • updated 2.2 years ago by Joe18k
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Comment: C: Pre_processing BAM file for variant calling using RNA-seq data
... @Kevin Blighe thanks for your comments, also can you give answer to the question I asked above? ...
written 2.6 years ago by ammarsabir1560
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Comment: C: Pre_processing BAM file for variant calling using RNA-seq data
... Also I want to ask why it is a problem? ...
written 2.6 years ago by ammarsabir1560
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Comment: C: Pre_processing BAM file for variant calling using RNA-seq data
... Yes it is hexaploid and I have to call variants on it sadly!!! ...
written 2.6 years ago by ammarsabir1560
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Pre_processing BAM file for variant calling using RNA-seq data
... I want to call variants using whole genome RNA-seq datasets of wheat. I have generated BAM files using STAR, I want to ask should I apply any post processing steps to these BAM files like Removing duplicates, removing reads based on quality scores etc before performing further downstream analysis? ...
alignment wheat_rna-seq rna-seq written 2.6 years ago by ammarsabir1560
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Error Running codeml
... Hi, I am trying to use codeml from PAML for phylogenetic analysis, but getting the same error again and again. The code used is given below: >>> from Bio.Phylo.PAML import codeml >>> cml = codeml.Codeml() >>> cml.tree = "species.tree" >>> cml ...
phylogeny alignment paml written 2.7 years ago by ammarsabir1560 • updated 2.7 years ago by Sishuo Wang200
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Comment: C: Extract Mitochondrial Genome Sequence from 1000 Genomes Data
... I am aware of ftp link for 1000 genome data, for the API link there are mostly tools related to data analysis and I doesn't found a tool or documentation to solve my problem. Is there any simple way to extract mitochondrial genome in fastq format from whole genome sequence of an individual from 10 ...
written 2.8 years ago by ammarsabir1560
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Comment: C: Extract Mitochondrial Genome Sequence from 1000 Genomes Data
... @genomx your answer provides the way to get fasta sequence but I want to extract sequence in fastq format from whole genome sequence. ...
written 2.8 years ago by ammarsabir1560
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Extract Mitochondrial Genome Sequence from 1000 Genomes Data
... Is it possible to extract mitochondrial genome sequence from whole genome sequence data available in 1000 genomes? If yes then how is it possible? I mean can we do it using a script or is there any online data extraction tool available for this purpose. ? ...
1000 genomes next-gen sequencing written 2.8 years ago by ammarsabir1560 • updated 2.8 years ago by GenoMax95k
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Reference genome for wheat/ Triticum aestivum
... I want to work on wheat genomics, for doing this I am not sure where to get the reference sequence for wheat because if you go to ensembl at this link [wheat genome][1] then there comes many things to download. Same happens for NCBI. I have downloaded a reference sequence from ensembl but that seque ...
genome next-gen sequencing written 3.1 years ago by ammarsabir1560 • updated 3.1 years ago by Emily_Ensembl21k

Latest awards to ammarsabir15

Popular Question 17 months ago, created a question with more than 1,000 views. For Mitoseek not installing correctly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Mitoseek not installing correctly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Algorithm for Getting per position nucleobases in python from bam file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Difference between Alignment quality and Mapping quality
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Error Filtering BAM file based on mapping qualities in python's pysam
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Mitoseek not installing correctly
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Extract vcf from 1000 genomes based on population and region
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Filter low quality reads in bam files
Popular Question 3.5 years ago, created a question with more than 1,000 views. For samtools creating difficulties in installtion

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