Salih Ulu Blog

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> > mygene expressionBarplot(mygene) >

Categories: Bioinformatics, Tuxedo

> csVolcano(genes(cuff_data), 'C1', 'C2') >

Categories: Bioinformatics, Tuxedo

> csScatter(genes(cuff_data), 'C1', 'C2') >

Categories: Bioinformatics, Tuxedo

> csDensity(genes(cuff_data)) Warning messages: 1: Removed 4109 rows containing non-finite values (stat_density). 2: Removed 4118 rows containing non-finite values (stat_density). >

Categories: Bioinformatics, Tuxedo

> cuff_data

Categories: Bioinformatics, Tuxedo

> library(cummeRbund) Zorunlu paket yükleniyor: BiocGenerics Zorunlu paket yükleniyor: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, […]

Categories: Bioinformatics, Tuxedo

6| Open a new plotting script file in the editor of your choice, or use the R interactive shell: salih-MBP:~ simacpro$ R R version 3.2.1 (2015-06-18) — “World-Famous Astronaut” Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (64-bit) R özgür bir yazılımdır ve KESİNLİKLE BİR GARANTİ VERMEZ. Belli koşullar altında tekrar dağıtımına izin verilir. Dağıtım detayları için ‘license()’ ya da ‘licence()’ girin. R, bir çok insanın katkıda […]

Categories: Bioinformatics, Tuxedo

Identify differentially expressed genes and transcripts ● timing ~6 h 5| Run Cuffdiff by using the merged transcriptome assembly along with the BAM files from TopHat for each replicate: salih-MBP:~ simacpro$ cuffdiff -o diff_out -b Bowtie2Index/genome.fa -p 4 -L C1,C2 -u merged_asm/merged.gtf my_rnaseq_exp/Drosophila_melanogaster/C1_R1_thout/accepted_hits.bam,my_rnaseq_exp/Drosophila_melanogaster/C1_R2_thout/accepted_hits.bam,my_rnaseq_exp/Drosophila_melanogaster/C1_R3_thout/accepted_hits.bam my_rnaseq_exp/Drosophila_melanogaster/C2_R1_thout/accepted_hits.bam,my_rnaseq_exp/Drosophila_melanogaster/C2_R2_thout/accepted_hits.bam,my_rnaseq_exp/Drosophila_melanogaster/C2_R3_thout/accepted_hits.bam You are using Cufflinks v2.2.1, which is the most recent release. [05:12:08] Loading reference annotation and sequence. Warning: couldn't find fasta record for '2LHet'! This contig will […]

Categories: Bioinformatics, Tuxedo

Create a file called assemblies.txt that lists the assembly file for each sample. The file should contain the following lines: ./my_rnaseq_exp/Drosophila_melanogaster/C1_R1_clout/transcripts.gtf ./my_rnaseq_exp/Drosophila_melanogaster/C1_R2_clout/transcripts.gtf ./my_rnaseq_exp/Drosophila_melanogaster/C1_R3_clout/transcripts.gtf ./my_rnaseq_exp/Drosophila_melanogaster/C2_R1_clout/transcripts.gtf ./my_rnaseq_exp/Drosophila_melanogaster/C2_R2_clout/transcripts.gtf ./my_rnaseq_exp/Drosophila_melanogaster/C2_R3_clout/transcripts.gtf  

Categories: Bioinformatics, Tuxedo

salih-MacBook-Pro:~ simacpro$ cuffmerge -g Bowtie2Index/genome.gtf -s Bowtie2Index/genome.fa -p 4 my_rnaseq_exp/Drosophila_melanogaster/assemblies.txt [Mon Jul 13 09:55:50 2015] Beginning transcriptome assembly merge ——————————————- [Mon Jul 13 09:55:50 2015] Preparing output location ./merged_asm/ [Mon Jul 13 09:55:53 2015] Converting GTF files to SAM [09:55:53] Loading reference annotation. [09:55:54] Loading reference annotation. [09:55:56] Loading reference annotation. [09:55:57] Loading reference annotation. [09:55:59] Loading reference annotation. [09:56:00] Loading reference annotation. [Mon Jul 13 09:56:02 2015] Quantitating transcripts […]

Categories: Bioinformatics, Tuxedo