Salih Ulu Blog

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Record differentially expressed genes and transcripts to files for use in downstream analysis (optional) ● Timing <5 min 16| You can use CummeRbund to quickly inspect the number of genes and transcripts that are differentially expressed between two samples. The R code below loads the results of Cuffdiff’s analysis and reports the number of differentially expressed genes: > library(cummeRbund) > cuff_data > cuff_data CuffSet instance with: 2 samples 14408 genes 25093 […]

Categories: Bioinformatics, Tuxedo

Compare transcriptome assembly to the reference transcriptome (optional) ● Timing <5 min 15| You can use a utility program included in the Cufflinks suite called Cuffcompare to compare assemblies against a reference transcriptome. Cuffcompare makes it possible to separate new genes from known ones, and new isoforms of 8 known genes from known splice variants. Run Cuffcompare on each of the replicate assemblies as well as the merged transcriptome file: $ find . -name transcripts.gtf > gtf_out_ […]

Categories: Bioinformatics, Tuxedo

Inspect the map files to count the number of reads that map to each chromosome (optional). From your working directory, enter the following at the command line: $ for i in *thout/accepted_hits.bam; do echo $i; samtools index $i ; done; $ for i in *thout/accepted_hits.bam; do echo $i; samtools idxstats $i ; done; The first command creates a searchable index for each map file so that you can quickly extract […]

Categories: Bioinformatics, Tuxedo

> expressionBarplot(isoforms(mygene)) >

Categories: Bioinformatics, Tuxedo

> > 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