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The code above can also be modified to write out small files containing only the differentially expressed genes. These files may be more manageable for some spreadsheet software than the full output files produced by Cuffdiff. The R snippet below writes a table of differentially expressed genes into a file named diff_genes.txt. > gene_diff_data sig_gene_data sig_gene_data write.table(sig_gene_data, 'my_rnaseq_exp/diff_genes.txt', sep='\t', row.names = F, col.names = T, quote = F) >

Categories: Bioinformatics, Tuxedo

> isoform_diff_data sig_isoform_data nrow(sig_isoform_data) [1] 265 > tss_diff_data sig_tss_data nrow(sig_tss_data) [1] 276 > cds_diff_data sig_cds_data nrow(sig_cds_data) [1] 270 > promoter_diff_data sig_promoter_data nrow(sig_promoter_data) [1] 132 > splicing_diff_data sig_splicing_data nrow(sig_splicing_data) [1] 130 > relCDS_diff_data sig_relCDS_data nrow(sig_relCDS_data) [1] 137 >

Categories: Bioinformatics, Tuxedo

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