Can CLC genomics read mapping files be used in Bioconductor/R and HTSeq-counts?

tdelaney · 02-20-2013, 11:05 AM

I have been using CLC Genomics for RNA-seq analyses. I am using the gaussian-based tests in CLC Genomics to detect differentially expressed genes but I am interested in using Bioconductor/R packages, such as DESeq. Can I use the exported bam/sam files produced from CLC's RNA-seq mapping tool in DESeq? Or do I need to use bam/sam files from another mapper such as TopHat? Additionally, can I use the bam/sam files from CLC as input into the HTSeq-count program? Thank in advance for you help.

Jeremy · 02-20-2013, 10:07 PM

You can use a sorted bam file as input for HTSeq-count (assuming CLC generates a regular bam file) to get read counts per sample and then merge these into a table of read counts per gene (rows) for each sample (columns) as input for DESeq.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
total number of counts with HTseq	oliviera	Bioinformatics	17	07-26-2013 08:33 AM
converting bam files to non-normalized read counts	lpn	Bioinformatics	4	10-09-2012 08:52 PM
htseq-count with warning for every read to represent all of zero counts in output	hibachings2013	RNA Sequencing	10	07-15-2011 11:19 AM
Mapping RNA seq using CLC Genomics WOrkbench	rururara	Bioinformatics	1	02-22-2011 12:35 PM
understanding HTSeq counts	nimmi	Bioinformatics	3	11-27-2010 08:24 PM

02-20-2013, 11:05 AM	#1
tdelaney Junior Member Location: Maryland Join Date: Nov 2010 Posts: 1	Can CLC genomics read mapping files be used in Bioconductor/R and HTSeq-counts? I have been using CLC Genomics for RNA-seq analyses. I am using the gaussian-based tests in CLC Genomics to detect differentially expressed genes but I am interested in using Bioconductor/R packages, such as DESeq. Can I use the exported bam/sam files produced from CLC's RNA-seq mapping tool in DESeq? Or do I need to use bam/sam files from another mapper such as TopHat? Additionally, can I use the bam/sam files from CLC as input into the HTSeq-count program? Thank in advance for you help.

02-20-2013, 10:07 PM	#2
Jeremy Senior Member Location: Pathum Thani, Thailand Join Date: Nov 2009 Posts: 190	You can use a sorted bam file as input for HTSeq-count (assuming CLC generates a regular bam file) to get read counts per sample and then merge these into a table of read counts per gene (rows) for each sample (columns) as input for DESeq.