RnaSeqAnalysis < Cores/BioinformaticsCore < TWiki
RNASeq Analysis tophat & cufflinks procedure 1. RNA-seq input files for cufflinks Suppose we are given the RNA-seq output files for two experimental conditions, Alpha and Beta. The format the files come in is FASTQ. The file Alpha will have tens of millions of lines like the following: @SOLEXA2:8:1:1:313#0/1 NGCCTCCCAAGTAGCTGGGATTACAGGTGCACATCACCAC <-- the RNA sequence read +SOLEXA2:8:1:1:313
TopHat :: Center for Bioinformatics and Computational Biology
tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis. We recommend that you download your Bowtie indexes and annotation files from this page. More information about Illumina's iGenomes project can be found here. Organism Data source Version Size Last Modified
Correcting p values for multiple tests where tests are correlated (genetics)
This is actually a hot topic in Genomewide analysis studies (GWAS)! I am not sure the method you are thinking of is the most appropriate in this context. Pooling of p-values was described by some authors, but in a different context (replication studies or meta-analysis, see e.g. (1) for a recent review). Combining SNP p-values by Fisher's method is generally used when one wants to derive an unique
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