View Full Version : Genomic Resequencing

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  1. Long-range PCR
  2. exon enrichment by PCR for resequencing
  3. SNP detection
  4. Genome rearrangement
  5. Getting Bowtie to work
  6. Difficulty mapping reads with non-reference allele?
  7. Agilent SureSelect - coverage of high GC regions
  8. Mutation discovery
  9. compare distribution of coverage in solexa data
  10. Next-gen sequencing of targeted genes with many DNA templates
  11. Procedure for paired-end with Agilent SureSelect array capture
  12. tigr rice genome v6.0
  13. BWA alignment for paired end reads
  14. samtools problems with reference in pileup file
  15. Multiple sample comparion or Segregation analysis
  16. Generate subset from BAM format
  17. merging bwa alignments
  18. attempting to sequence human MHC region
  19. pileup format- what is ^F
  20. IMAGE input files
  21. Assisted assembly of contigs into supercontigs/chromosomes
  22. how to determine a snp ?
  23. SNP or not
  24. Samtool merge problem
  25. SOAPsnp pileup viewer
  26. BWA mapping quality scores?
  27. Getting a full annotation onto a consensus sequence in CLC Genomics Workbench
  28. exome sequencing track with agilent
  29. what does "XT:M" in BWA output mean?
  30. mpileup failed when using samtools.pl varFilter
  31. Sure Select Exon Capture
  32. bam output file to psl file
  33. Why MAQ consensus seq better than SAMtools consensus ??
  34. what does it means
  35. Complete Genomics Releasing 60 Human Genomes
  36. Why 30X
  37. Lots of false positives with SAMtools SNP discovery
  38. Does human genome seq consist of telomere seq?
  39. samtools pileup base quality
  40. Understanding BAM format.
  41. Real SNPs discovered with samtools v0.1.7 disappear with v0.1.8
  42. Doing things with CrossBow output ?
  43. Exome Sequencing with NimbleGen SeqCap EZ v2
  44. What sort of library and how many reads for SV detection?
  45. Calling STRs using SAMTools?
  46. designing SureSelect baits in repetitve regions
  47. calling SNPs in haploid genomes
  48. SNP calling for captured sequence data
  49. Analyzing Targeted Resequencing data with Galaxy
  50. Coverage assessment
  51. data size and system requirement
  52. Appropriate Reference Format
  53. Most commonly used tools
  54. Agilent human exon coverage plots
  55. Quality control of genomic resequencing data from a HiSeq
  56. Genotyping platform for fine-mapping a region
  57. Planning a cancer exome sequencing project
  58. Illumina fragment length distribution
  59. Question concering deletions and inversions inferred from PE-sequencing
  60. SNP calling from a reference sequence
  61. %varfreq homozygote off to 30%
  62. Coverage of reads not homogenous (sureselect target enrichement)
  63. Calling structural variants (CNVs) with single-end reads
  64. Qs in exome sequencing data analysis
  65. Help picking up an abandoned sequencing project
  66. Index between genome and mRNA
  67. Strange Ti/Tv ratios in GATK VariantEval report
  68. Sequencing of Epstein-Barr virus genome in a mixture of total human DNA
  69. Optimising SRMA for speed in the absence of a cluster
  70. samtools mpileup questions
  71. Crossbow alignment format
  72. GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment
  73. Reactions vs. Samples
  74. pysam IteratorSNPCall output different than the samtools mpileup
  75. HeLa cell genome
  76. Differences in Consensus Sequences
  77. samtools mpileup using -l or -r
  78. TCGA : capture vs. exome question?
  79. Novoalign with GATK recalibration
  80. effect of mRNA contamination
  81. soapSNP doesn't produce output, just consumes CPU cycles
  82. No peaks
  83. Resequencing project: What type of sequence to include per gene?
  84. Illumina vs. Agilent Exome enrichment - higher false positive rates
  85. Exome sequencing
  86. Targeted resequencing - open source
  87. Samtools mpileup_Paired Tumoral / Germline_keep only somatic mutations
  88. QTL location?
  89. Exon Sequencing of Human Chromosome X: Im in serious trouble
  90. dwgsim for single ends simulation
  91. Need help identifying SNPs and allele frequencies
  92. coverage calculation
  93. Genome resequencing and phylogenetics
  94. detecting deletion in amplicon sequencing of mixed population
  95. New targeted resequencing technologies and resources for the community
  96. some basic queries (mapping)
  97. wet lab Validation of a large number of SNPs
  98. Astronomical quotation
  99. Batch effect, SNPs
  100. expected mutation rates?
  101. Number of Mapped reads
  102. Enrichment for Cancer research
  103. Exome capture validation
  104. VCF to Circos format(s)
  105. Pre-Capture Pooling with Nimblegen SeqCap EZ v3: SNP detection quality?
  106. Bowtie2 - segmentation fault due to --sam-RG
  107. dbsnp135 vcf on an alignment with hg19
  108. In a 'typica' human exome sequencing experiment...?
  109. Bowtie2 truncated output
  110. All Exome using amplified gDNA strategy ???
  111. heterozygosity to homoszygosity ratio
  112. indel realignment by GATK: IndelRealigner or LeftAlignIndels
  113. Indel analysis (SAMtools:pileup or mpileup)
  114. question about using samtools
  115. indel discovery methods?
  116. bwa reference genome alignment
  117. CNV Boundary Estimation
  118. any recommandation on variant caller for SOLiD data ?
  119. saving samtools mpileup output from a cluster
  120. Simulation of inversions and translocations
  121. Bowtie vs Bowtie2
  122. question about CREST PCR template file
  123. how to identify SNPs and indels between two samples
  124. Optimal bandwidth for kernel CNV estimation
  125. [bwt_restore_sa] SA-BWT inconsistency: seq_len is not the same. Abort!
  126. Creating "Consensus" Sequence between Reference and Mapped Reads
  127. Paternal testing microsatellites
  128. Retrieving reads with SNPs
  129. seeking pool-seq experimental design advice
  130. Request for Example of "consensus diploid sequence" required by PSMC (Li & Durbin)
  131. vcfutils.pl varFilter removes INDELs even with default override
  132. Haplotypes reconstruction using 454 data (single-end reads)
  133. approaches for discovering proximal snps?
  134. How to randomize for sample multiplexing and flow cell placement?
  135. Whole genome sequencing
  136. Exome Sequencing vs Target Region Sequencing
  137. Comparing Kmer distribution between samples
  138. Exome sequencing analysis problem
  139. Whole Genome Re-sequencing concept
  140. The depth in .vcf file
  141. Problems when calling SNPs using samtools mpileup
  142. Tophat with bowtie2
  143. Best tools for SNP calling with resequenced mutant?
  144. Illumina vs NimbleGen for exome sequencing
  145. How to detect random mutations by genome resequencing?
  146. Tophat RnaSeq(20-36bp)bp reads
  147. Duplicate SNPs
  148. Select only one sample in 1000 Genomes whole genome VCF
  149. Tips for writing an own aligner
  150. Whole genome analysis - how do you guys do it?
  151. VCF row validity
  152. basic doubts in mapping
  153. Variant discovery in experimental evolution
  154. transposon/insertion sequencing techniques
  155. Illumina TruSeq Cancer Panel p53 Coverage
  156. When the reference sequence isn't perfect
  157. run psmc in parallel?
  158. Kits for targeted resequencing
  159. TopHat-Fusion with DNA-Seq reads?
  160. Whole Genome Amplification for Cancer Study
  161. Number of variants from mouse exome looks very small
  162. dindel how to merge library files in pooled setting
  163. how to analyze whole genome sequencing data (new genome assembling)?
  164. Vcf genotypes for RILs
  165. Sequence substitution tool for resequecing
  166. Duplex Sequencing on MHC
  167. Scaffold end SNPs and artifact checks
  168. How to read FASTQ files?
  169. XA tag from bwa
  170. bowtie2: aligning multiple input files
  171. lowercase and n in consensus sequences by mpileup
  172. BWA sai file is having different sizes for paired end
  173. Calculating and separating reads per chromosome
  174. Indexing reference genome hg.19 ?
  175. About samtools sort
  176. large indels in targeted sequencing
  177. gene copy number -k parameter
  178. Fungal Resequence, high identity, which model for phylogeny?
  179. Questions for barcode file splitting, forward/reverse data sorting
  180. best way to re-sequence a few Mb of genomic sequences
  181. Questions in calling SNPs from RNA-seq reads
  182. SNPs to genotypes file?
  183. GATK-usage-ERROR-Helpreg
  184. Remapping
  185. Best pipeline for annotation Helicobacter pylori with clc genome
  186. CNS file format
  187. simulate ngs reads using mutation, frequency , quality etc. parameters
  188. Haloplex and SureCall
  189. finding deletions of length 20 - 50bp from 100bp reads
  190. How many genes in human genome?
  191. What is the best way to perform ultra-deep targeted sequencing of few samples?
  192. Importing multiple contigs annotations from maker to webApollo
  193. SNP density
  194. pooling strategy for selective sweeps
  195. PCR amplifying microsatellites (short tandem repeats) for sequencing
  196. Targeted resequencing/enrichment for low complexity regions
  197. SNP Filtering
  198. Randomly sampling loci from multiple resequenced
  199. 1k genomes and VCF: slow processing of individual genome
  200. question about bcftools merge
  201. Mouse population genetic data
  202. Getting error Streaming Command failed! with mouse chromosome17 example
  203. Compare difference capture technologies
  204. Eliminating dry-down/speed-vac step in Nimblegen hybridization capture setup
  205. BWA-GATK pipeline showing weird results upon visulisation
  206. Dwgsim reads not generating header properly
  207. Strange strand bias and unusual depths
  208. CNV and INDEL calling
  209. Missing variant after HaplotypeCaller joint calling
  210. Why BWA output didn't agree with bowtie2
  211. bwa mem and pindel
  212. Adding GT tag to Strelka Output
  213. Trying to check plasmid alignment
  214. Cancer Exome-Seq data without matched Normal
  215. How to construct chromosomes from scaffolds of a subspecies
  216. Haplotype caller 3.2 versions not calling a true variant
  217. Variant found in priming site
  218. Allele frequency in sample below 10%
  219. Negative start position bed file
  220. A union of alleles file for glia
  221. SNV ignored by bcftools
  222. Nextseq - too much data for base space and any de novo assemblers
  223. Best alternative for Nextera Indices for multiple amplicon resequencing experiment ?
  224. vcfutils.pl varFilter -D option setting
  225. plink2 to EIGENSOFT .geno conversion
  226. Genomic NGS sequencing to find sponaneous bacterial mutations
  227. WGS batch effects
  228. What are key factors to consider while planning pooled DNA sequencing
  229. Publicly available Summary Statistics
  230. CNV by read_depth approach
  231. delins in VCF
  232. --min-var-freq Varscan2mplieup
  233. SOAPindel with bwa-mem
  234. Variant calling from paired/unpaired reads
  235. What information can I extract from a large dataset of a single gene
  236. mutations file
  237. Trim to target in exome-seq
  238. How to estimate total genetic diversity from a sequenced population?
  239. Key Considerations for Whole Exome Sequencing
  240. Targeted resequencing for VAF confidence - how avoid amplification bias?
  241. psmc bootstrap
  242. ethnic databases of hg19
  243. Genomic Inflation Factor Less than 1 in GenABEL
  244. does read order influence bwa mapping?
  245. freebayes haplotype calling (phased variants)
  246. Variants inside and outside of target region - what's the difference?
  247. Looking for structural variants with paired-end sequencing data
  248. Phaseolus vulgaris genome
  249. Abnormaly amount of reads
  250. fastq.gz size for human WGS coverage calculation