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  1. differential gene expression - Illumina
  2. mapper which work with ambiguous bases
  3. are these motifs same ?
  4. 1000 genomes raw data should be filtered?
  5. Wig correlation
  6. RnaSeq differential expression
  7. Restriction Digests with ambiguity
  8. Count Base Pairs?
  9. Pseudo-molecule
  10. samtools converting sam to bam filtering
  11. Do I need remome the reads aligned >1 times and how?
  12. Using coverageBed in bedtools
  13. how to parse reads containing a particular sequence in any orientation
  14. Removing repeats but accounting for them
  15. Tallying BLAST results
  16. The easiest/fastest way to get from BAM to TPM or RPKM
  17. SHRiMP mapping algorithm
  18. Mouse somatic variants (COSMIC equivalent)
  19. Fast flow cells and Allpaths
  20. BWA insert size distribution too large
  21. DEXSeq error: 'SAM optional field tag NH not found'
  22. library size of TCGA RNASeq data
  23. Sam to Bam using bowtie and using the shell script
  24. Do I need to create an index for my reference genome?
  25. samtools rmdup leaves unpaired mates
  26. Finding SNPs in a particular chromosome
  27. awk - need help comparing 2 files
  28. new tool for bigWig data
  29. COG functions to categories
  30. find the second patient
  31. How to find alteranative TSS between two group of samples
  32. still too many differentially expressed genes.
  33. do number of queries affect the result of blat?
  34. Can we show by manually analysis why Cuffdiff and edgeR gives different results?
  35. Selection of sequences
  36. Bowtie2: partial mapping of assembled contigs?
  37. RNASeq Differential Gene Expression with two-sample Mann-Whitney test on FPKM?
  38. samtools view region not working properly
  39. questions on the three index files for RNAseq analysis
  40. R mateys! Which is Best FDR ?
  41. Differential Coverage
  42. SOAPdenovo pregraph read counts
  43. DESeq2 - varianace stabilized pseudocounts and PCA plot
  44. Puzzling tophat problem
  45. variant filtering of mouse whole exome sequencing
  46. Experiences with bioinformatics job prospects in different cities
  47. Illumina nextra sequencing
  48. Illumina - mapping genome on reference - how to extract assembly?
  49. Sam to Bam Conversion Failing ****
  50. easy way to assemble 50% of reads?
  51. FastQC for paired-end, alignment stats
  52. Calling tumor CNVs without normal as control?
  53. QC'ing NGS data
  54. perfect match with bowtie/bowtie2
  55. Parsing Smith-Waterman Alignment EMBOSS
  56. RNA-seq with UniGene sequences as target
  57. Picard ValidateSamFile: Problem with NM tag
  58. Which bam file is what I need to count reads?
  59. 1000 genomes human reference
  60. How to find the # of reads and # of bases being removed?
  61. detect Isoforms using Cufflinks and Cuffdiff
  62. how to evaluate if the replicates are good
  63. Evaluating overdispersion in CummeRbund
  64. in silico RAD seq double digest fragment calculation
  65. Quantifying ChIP-seq peak density in gene bodies
  66. DESeq NB test for samples without biological replicates
  67. vcf-consensus for individuals from 1000G
  68. SGD liftOver chain files issue
  69. Gene-level association test based on SNP data
  70. Refseq FPKM values for genes (hg19)
  71. b2g4pipe returns only a .annot file... What about the .dat file?
  72. Is my parameter choice for HTSeq-count is right?
  73. DEXseq file loading flattened
  74. When is a gene considered unexpressed?
  75. Samtools multisample SNP caller
  76. How do I use SolexaQA?
  77. Trinity will not install properly on Mac OS X
  78. open source code for WGS ancestry painting?
  79. HPC cluster : make error : make[2]: *** [bundles.o] Error 1
  80. How do I calculate tetranucleotide frequencies?
  81. Staden gap5 : Template Plot Colors
  82. Alignment trouble with pair-end reads
  83. Parsing indels in a pileup
  84. Qustion about miRNA-Seq normalization and analysis
  85. What to include in my count table(s) for DESeq
  86. Convert .gff3 file to 12-column .bed file
  87. bwasw soft clipping of exact matches
  88. Strangely low proportion of mapped miRNA reads
  89. How to get the Gene names to GO terms for bacteria and archaea
  90. How to calculate coverage for transcripts?
  91. Bam to Fastq on discordant mate pairs
  92. How to use Sapred and PolyPen2
  93. targeted resequencing data analysis tool
  94. How to correctly choose Read Groups ?
  95. ARDEN gives wrong sequence result
  96. inconsistent .bam file statistics
  97. why doesn't this linux command work for me?
  98. Do I need adding 1 pseudocount (prevent dividing by 0)?
  99. Parsing a GenBank file
  100. VCF file from aligned fasta?
  101. htseq error
  102. What does "%in%" mean?
  103. bamtools-2.3.0 will not work
  104. Jellyfish problem
  105. How many reads are needed for RNASeq experiments?
  106. CLC paired read orientation- max. and min. read distance
  107. BLAT of sequence to dog/human reference confounding
  108. Adding features to a multi entry genbank
  109. 3'UTR Isoform from Cufflinks
  110. fastx-clipper to remove adapters problem
  111. perl script to exact sequences by name list
  112. Copy number exome benchmark data
  113. FDR and underpowered p-values
  114. Problem with the tol CoNiFer
  115. How to add heater to the hts-count output file in linux?
  116. Dexseq warnings: Failed to fit dispersion for gene
  117. Problems using wgsim in Linux/Ubuntu
  118. Generate consensus from MultiFasta
  119. PSGInfer: question for bioinformatics/statistics folks
  120. Understanding samtools mpileup consensus
  121. tmap - set up read length to map?
  122. difference between rr ff and rf reads
  123. Whole genome alighment
  124. RNA Seq Simulator
  125. Gem index and mapping
  126. RNA secondary structure formats
  127. cutadapt
  128. Ensembl database fetch sequence problem
  129. How to adjust the p values of edgeR?
  130. how to summarize information for a gene from bam file
  131. high levels of broken read pairs?
  132. sus scrofa (pig) KEGG pathways: where to find...
  133. Cufflinks novel gene discovery
  134. variation analysis in NGS data
  135. HTSeq 'gene_id' attribute error
  136. Using GenomicRanges
  137. read mapping
  138. Adapter sequence trimming
  139. Differential Expression Using mixed libraries (truseq, nextera)?
  140. SPAdes contigs
  141. snpEff error
  142. bwa mem stringent mapping
  143. Best hit alignment in offline Blast
  144. Importance of lane information in Picard and GATK
  145. bowtie mapping
  146. Creating bacterial reference genomes
  147. Ref.-guided consensus using alt. alleles
  148. splitting the .sra file
  149. looking for help for NCBI primer blast
  150. construct annotation files
  151. MetaPhyler
  152. Quality trimmer
  153. Changing the strand in a Bam/Sam file
  154. How to extract assembled transcript sequence from RNA-seq data instead of ref genome?
  155. miRNA analysis
  156. How to use codeml to calculate ω ratios of internal branches "iteratively"
  157. Gplink data analysis EMP1
  158. Combinatorial exom seq data
  159. Dr
  160. fewer reads R1 than R2 bowtie2
  161. Tophat2 Multiple alignment discrepancy
  162. Obtaining Random Sequences from Given Taxonomic Grouping
  163. perl script for fetching lines, if a pattern is given
  164. python script to bast NCBI's SRA database
  165. how to identify blast hits with only 1 HSP (not limit the number of HSP)
  166. CNAseg, local variability
  167. 1000 Genome data download for help?
  168. adapter remove
  169. cutadapt
  170. Illumina - Paired End Barcode Split + Mip trimmer
  171. SOAP pipeline
  172. seq pathway analysis
  173. get Gene Coordinates of human genes names
  174. Exome Variant server vcf files
  175. what is wrong with the gage?
  176. bowtie2: error reading ebwt[] array
  177. Finding the coordinate of combined bed file
  178. cufflinks 2.1.1 on Mac mini
  179. run cuffmerge gives such error message
  180. Too many Variants called by HaplotypeCaller GATK
  181. Normalizing RNA-seq within samples
  182. Mapping HiSeq to Proteins
  183. Tool for extending reads ?
  184. The easiest way to produce the normalised counts in edgeR
  185. Picard MergeBam Alignment issue
  186. FastQC Overrepresented Sequences problem
  187. bowtie mapping with R1&R2 and R1
  188. Chimerscan 0.4.5 runs for days and then system kills it
  189. Determine ethnicity from exome sequence
  190. FASTA to BAM for IGV visualization
  191. how does insertion/deletion detected?
  192. how to download data from “The European Genome-phenome Archive”?
  193. VCF tools, define populations
  194. TopHat (v2.0.4)error
  195. graph for relationship of homologous genes
  196. A django-based frontend to cuffdiff output
  197. BWA XT:A:U and XA for same read?
  198. Intersect BAM files from alignments to human and mouse
  199. picard CollectAlignmentSummaryMetrics
  200. min length and max length with fastx tookit
  201. cuffmerge
  202. Blast Results GO Mapping
  203. GSNAP error
  204. cufflinks
  205. coverage calculation - Bedgraph files
  206. latha
  207. BEAGLE errors: Allele not in marker file / Number of fields in .gprobs isn't %3
  208. Mother of Ribosomal Dtatabses ?
  209. Isolating barcoded reads in .Bam file
  210. CLC- extracting sequences based on coverage/length
  211. DESeq2 error: varianceStabilizingTransformation error
  212. Is there an algorithm that align two sequences?
  213. Viral Qausispecies analysis- tips and tricks? PLEASE HELP!
  214. HTSeq issue with stdout/stdin
  215. How to find the abbreviation of gene name
  216. tophat output
  217. confused about the pileup data
  218. MeDIP Seq - Peak Strand
  219. puzzle with gmapper -M mirna (shrimp)
  220. rna-seq tiling reads
  221. bowtie: extra parameter error
  222. samtools filter PE reads on mapping quality of only one of the reads
  223. SNP calling from multiple genotypes
  224. bowtie2 fragment length
  225. Tophat2 with GFF3 annotation fails to produce Bowtie index.
  226. script suggestion (SAM file)
  227. tophat : sam-flag 115 = properly-paired + read.reverse + mate.reverse ?
  228. bioinformatics workstation
  229. Alternative to blast?
  230. bwa sampe: the read group line is not started with @RG
  231. is ok to analyse 21 bp DGE tags with tophat-cufflink pipeline?
  232. [cufflinks] cufflinks fail to annotate gene_id correctly
  233. visualising the alignment between reads and its template
  234. which denovo assemble to use for assembly of meta-transcriptome data
  235. Combination of paired-end and single-end samples in Chip-seq TF study
  236. Quick Interpretation of FastQC output
  237. Number of sequences in NCBI nt database
  238. Replicates correlation for differential expression
  239. Gene Ontology analysis tools
  240. tophat2 bowtie option help
  241. Breakdancer output file question
  242. Need help with Trinity bowtie utility
  243. Why could I not load gage?
  244. Newbler GSmapper output numMappedReads 2 results
  245. Looking for sample MiSeq output
  246. mpileup to vcf
  247. more problems with RSEM in Trinity build
  248. augustus gene finder
  249. What genesets can I use for pathway analysis of honeybee seq data?
  250. How to make simulated exome sequencing data with known mutation