PDA

View Full Version : Bioinformatics


Pages : 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 [54] 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80

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