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