User: zam.iqbal.genome

gravatar for zam.iqbal.genome
Reputation:
1,580
Status:
Trusted
Location:
United Kingdom
Website:
www.well.ox.ac.uk/iqbal
Last seen:
2 years, 10 months ago
Joined:
5 years, 6 months ago
Email:
z***************@gmail.com

about me

Posts by zam.iqbal.genome

<prev • 93 results • page 1 of 10 • next >
0
votes
1
answer
1.4k
views
1
answers
Answer: A: Benefit of platinum genomes in WGS experiment
... See here http://www.illumina.com/platinumgenomes/ Illumina have basically done variant calling on this 17-member pedigree with their best sequencing protocols and very high depth, and then called variants with a large number of state of the art callers (GATK, Cortex, Freebayes, Isaac etc etc), and ...
written 2.9 years ago by zam.iqbal.genome1.6k
2
votes
3
answers
1.9k
views
3
answers
Answer: A: bam file assembly (1000 genomes)
... One of the things the 1000 Genomes (led by Richard Durbin's group) is doing is building a "read server", which effectively allows you to make web queries for primers (or kmers or haplotypes) and it will tell you which sample has them. Right now it's not yet publicly available, but it will be soon. ...
written 3.1 years ago by zam.iqbal.genome1.6k
1
vote
3
answers
1.9k
views
3
answers
Comment: C: bam file assembly (1000 genomes)
... If the longest thing you saw was 300bp then you looked in the wrong VCF file - they 1000g has called stuff that is many tens of kb long. I'll try and find a path for the latest VCFs ...
written 3.1 years ago by zam.iqbal.genome1.6k
0
votes
2
answers
1.5k
views
2
answers
Answer: A: Novel Sequence Insertions 1000 Genomes Project
... In the 1000G pilot paper (A map of human genome variation from population-scale sequencing. The 1000 Genomes Consortium. Nature 467,1061-73 (2010)) , we assembled 164 humans with Cortex and assembled novel sequence. The file is here: ftp.1000genomes.ebi.ac.uk:/vol1/ftp/pilot_data/paper_data_sets/a_ ...
written 3.6 years ago by zam.iqbal.genome1.6k
2
votes
2
answers
2.3k
views
2
answers
Answer: A: Variant Discovery In Bacteria
... Sorry for the self-advertising, but this pipeline for bacteria calls SNPS, indels and structural variants http://bioinformatics.oxfordjournals.org/content/29/2/275.full.pdf+html It was developed after prototyping in this paper: http://www.pnas.org/content/early/2012/02/27/1113219109 and also has b ...
written 3.7 years ago by zam.iqbal.genome1.6k
1
vote
1
answer
2.1k
views
1
answers
Answer: A: Fasta Sequence For Each Hla Alleles
... I think the resource you want does not exist yet. IMGT contains information on the HLA classical genes restricted to 2 exons for class I, and 1 for class II (I think - don't quote me on class II). The _nuc files are from CDS (so with introns spliced out) and the _gen files are from genomic sequence ...
written 3.7 years ago by zam.iqbal.genome1.6k
1
vote
3
answers
2.0k
views
3
answers
Comment: C: Are There Population-Specific Snps Included In The 1000Genomes Vcf Files?
... No problem! I found it hard to keep up with the data except when I was tracking all the conference calls. Z ...
written 3.7 years ago by zam.iqbal.genome1.6k
4
votes
3
answers
2.0k
views
3
answers
Answer: A: Are There Population-Specific Snps Included In The 1000Genomes Vcf Files?
... Hi there There is no filter to remove population specific SNPs, that's why you can't find a reference to it. It is rare to find, for example, SNPs at medium frequency in Europe and absent from all other populations. Singleton SNPs are by definition also population specific, but in the process of tr ...
written 3.7 years ago by zam.iqbal.genome1.6k
0
votes
0
answers
678
views
0
answers
Forum: Job Available In Zam Iqbal'S Lab In Oxford - Senior Web Application Developer
... Hi All I'm recruiting a Senior Web App Developer to my team here in Oxford, to work with microbiologists, clinicians and public health in the UK and USA on some species-specific web apps for accessing maps of global genetic diversity. This is a very exciting time to get involved and to play a key r ...
forum bacteria web job written 3.8 years ago by zam.iqbal.genome1.6k
2
votes
0
answers
777
views
0
answers
Forum: Job Available In Zam Iqbal'S Lab In Oxford - Senior Web Application Developer
... Hi All I'm recruiting a Senior Web App Developer to my team here in Oxford, to work with microbiologists, clinicians and public health in the UK and USA on some species-specific web apps for accessing maps of global genetic diversity. This is a very exciting time to get involved and to play a key r ...
forum bacteria web job written 3.8 years ago by zam.iqbal.genome1.6k

Latest awards to zam.iqbal.genome

Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Why Insertion Are Hard To Find By The Alignments Of Reads Than Deletion ?
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Advice For Newcomers To The Bioinformatics Field
Appreciated 3.7 years ago, created a post with more than 5 votes. For Phd Position In Zam Iqbal'S New Lab/Group In Oxford
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Decoy In Reference Assembly
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Why Insertion Are Hard To Find By The Alignments Of Reads Than Deletion ?
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Advice For Newcomers To The Bioinformatics Field
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: Decoy In Reference Assembly
Good Answer 3.7 years ago, created an answer that was upvoted at least 5 times. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Guru 3.7 years ago, received more than 100 upvotes.
Supporter 3.7 years ago, voted at least 25 times.
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Why Insertion Are Hard To Find By The Alignments Of Reads Than Deletion ?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Most Appropriate Software Detect Population Specific Structural Variation In Mul
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Advice For Newcomers To The Bioinformatics Field
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Retrieving Individual Genomes From 1000Genomes Project
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Tools For Combined Genome Variation Analysis Of Short Sequencing Reads For Sever
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: How To Generate Two Haplotypes Using Velvet
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Why Are There More Non-Synonymous Snps Than Synonymous Snps In The 1000 Genomes
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Decoy In Reference Assembly
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Insertion Detection Tools
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Are There Population-Specific Snps Included In The 1000Genomes Vcf Files?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1492 users visited in the last hour