User: kezcleal

gravatar for kezcleal
kezcleal130
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130
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United Kingdom
Last seen:
2 years, 10 months ago
Joined:
4 years ago
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k*******@hotmail.com

Posts by kezcleal

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Reads in BAM file overlapping coordinates
... Hi You can user Counter from the collections module to do the counting. from collections import Counter counts = Counter(sequence) Here is a one liner which should work: all_bases = [Counter([aln.seq[i] for i in range(len(aln.seq)) if aln.qual[i] > 30]) for aln in bamfile.fetch('chr5', 1234, ...
written 3.0 years ago by kezcleal130
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Comment: C: Displaying somatic mutational signatures
... Thanks, I will give this a try ...
written 3.3 years ago by kezcleal130
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Displaying somatic mutational signatures
... Sorry if this is a very basic question. Ive been following the methodology of Alexandrov et al.,2013 (see http://cancer.sanger.ac.uk/cosmic/signatures) to find the mutational signature of a cancer sample and have become confused about how mutational signatures are supposed to be displayed on a graph ...
genome snp written 3.3 years ago by kezcleal130 • updated 3.3 years ago by trausch1.2k
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How to get log ratio from cn.mops segplot function
... I have been using cn.mops to call CNVs, and I have been using a useful function 'segplot' which makes a nice graph of the log ratio of the read counts (y-axis) vs the genomic position on the x-axis. An example is given in the documentation http://bioconductor.org/packages/release/bioc/vignettes/cn.m ...
R next-gen written 3.7 years ago by kezcleal130 • updated 3.6 years ago by Biostar ♦♦ 20
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BQSR using GATK without dbsnp
... Hi, I have run the base quality score recalibration (BQSR) tool from GATK but for the known sites parameter I used only two databases: Mills_and_1000g_gold_standard_indels 1000G_phase1.indels  I realise I should possibly also have included the dbsnp_138 database in this list. Is it necessary to r ...
sequence next-gen snp written 3.9 years ago by kezcleal130 • updated 2.2 years ago by youcai50
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Comment: C: Tumor clonality algorithms
... My initial hunch was to use PhyloWGS ...
written 3.9 years ago by kezcleal130
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Tumor clonality algorithms
... I am interested in assessing the clonality of a tumor sample I have which is also paired with a normal tissue control from the same patient (~30x coverage). Specifically, I would like to know if there are any significant sub-clones present within the tumor sample. I have come across numerous tools ...
ngs snp sequencing written 3.9 years ago by kezcleal130 • updated 8 months ago by sm.hashemin60
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Comment: C: Advice for high quality scores for GATK
... Thank you. The sequencing of these samples was outsourced to BGI in china although I am unaware what platform was used. ...
written 3.9 years ago by kezcleal130
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Advice for high quality scores for GATK
... I am using data which appears to have a higher than expected distribution of quality scores.  From picard-tools: QualityScoreDistribution.jar, the highest scores are over 70: http://s483.photobucket.com/user/Kez_Cleal/media/1_DB31.qualDist_zpsf2xjcckq.png.html When I try and use GATK it complains ...
next-gen sequence written 3.9 years ago by kezcleal130 • updated 3.9 years ago by Devon Ryan90k
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Good tool for viewing Multiallelic vcf/bcf files
... What would be a good tool for viewing vcf files with multiple alleles per site? IGV appears to only show homo/heterozygous with respect to the reference. Does any software display allele frequencies, or the allele spectrum in a user friendly format?  ...
sequence snp written 4.0 years ago by kezcleal130 • updated 3.9 years ago by Zaag720

Latest awards to kezcleal

Student 2.9 years ago, asked a question with at least 3 up-votes. For Tumor clonality algorithms
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Should I remove Kmers identified in FastQC?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Tumor clonality algorithms
Student 3.4 years ago, asked a question with at least 3 up-votes. For Tumor clonality algorithms

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