Tool to take mapping to gene list

jarthur · 01-16-2013, 04:04 PM

Hello all,

I am relatively new to NGS and have just mapped a series of reads to a genome using Bowtie2. As I understand, the SAM/BAM output contains the information telling me where the reads map to the genome. I now want to:

a) transform this to a list of regions where reads map i.e., combine all the overlapping reads that map to one part of the genome into a starting position (bp), ending position (bp), and the number of reads that map to that region

b) cross-reference that list of regions against the genome annotation to identify whether that collection of reads maps to an exon, intron, etc. and, if an exon, extract the relevant gene and transcript id

I am sure there must be a tool for this - probably several! I am interested to know what people use? Any relative advantages/disadvantages, key tips or tricks, etc., would also be helpful.

Thanks for your help.

Regards,

Jonathan

chadn737 · 01-16-2013, 04:31 PM

I'm assuming this is RNA-seq data? Are you wanting simply a count of reads mapping to a feature?

If so, then there are a variety of tools that can accomplish this. The two most commonly used are probably BEDtools and HTSeq-count.

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01-16-2013, 04:04 PM	#1
jarthur Junior Member Location: Australia Join Date: Feb 2012 Posts: 3	Tool to take mapping to gene list Hello all, I am relatively new to NGS and have just mapped a series of reads to a genome using Bowtie2. As I understand, the SAM/BAM output contains the information telling me where the reads map to the genome. I now want to: a) transform this to a list of regions where reads map i.e., combine all the overlapping reads that map to one part of the genome into a starting position (bp), ending position (bp), and the number of reads that map to that region b) cross-reference that list of regions against the genome annotation to identify whether that collection of reads maps to an exon, intron, etc. and, if an exon, extract the relevant gene and transcript id I am sure there must be a tool for this - probably several! I am interested to know what people use? Any relative advantages/disadvantages, key tips or tricks, etc., would also be helpful. Thanks for your help. Regards, Jonathan

01-16-2013, 04:31 PM	#2
chadn737 Senior Member Location: US Join Date: Jan 2009 Posts: 392	I'm assuming this is RNA-seq data? Are you wanting simply a count of reads mapping to a feature? If so, then there are a variety of tools that can accomplish this. The two most commonly used are probably BEDtools and HTSeq-count.