[swbarnes2]

hi,
very thanks for that ,now I have BAM files and how can I extracting exon reads from BAM using Samtools?
any ideas will be awesome!


Thanks,
huili

I assume that you have aligned reads to the whole genome, and now want to filter for only those reads that hit exons?

Get a .bed file of exon boundaries, and use BEDTools intersectBed to filter the .bam;

[lhlbio]

I assume that you have aligned reads to the whole genome, and now want to filter for only those reads that hit exons?

Get a .bed file of exon boundaries, and use BEDTools intersectBed to filter the .bam;

Yes, some exom sequencing are what I have done ,now I can try to filter my exom reads by applying your command ,but I havn't use BEDTools before ! now I must learn someting !
thanks very much!

[lhlbio]

lhlbio,

If you have the annotations for your reference you can collect them all in the: 'chr1:start-end' format and then run this command:

samtools view aln.sorted.bam chr2:20,100,000-20,200,000 [region2 [...]]

If that doesn't work because there are too many arguments; I'd do each one separately in a shell script and then 'samtools merge' the results.

very thanks, I use the command "samtools view aln.sorted.bam chr2:20,100,000-20,200,000 [region2 [...]]",and it does work,but I can't understand it on the screen of linux operation interface.
if I can write it into some files as using "R" do? or other methods ? any help will be appreciated!