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ardmore 11-09-2011 11:18 AM

Can I view output the entire genome data?
Suppose I have a sam file?
Can I use samtools command to get whole genome data?


dpryan 11-09-2011 12:49 PM

Could you describe what "whole genome data" means?

ardmore 11-09-2011 12:51 PM

If we use samtools, we can select chromosome.
The entire means from chr1 to chr 23.

swbarnes2 11-09-2011 12:57 PM

By default, samtools view will convert the whole .sam file into a .bam. Just don't add a chromosome name to the command line, and you'll get everything.

ardmore 11-09-2011 02:07 PM

Can we identify the start and the end position?
I just guess that start from 0 and end with a big number.

dpryan 11-09-2011 02:12 PM

If you want the whole thing then don't add start or end positions. From reading the man page, I gather that specifying start and end positions without indicating an actual chromosome would confuse things.

jbrwn 11-09-2011 02:21 PM

to get everything just:

samtools view .bam
to get everything and the header:

samtools view -h .bam
for .sam, add the sam option

samtools view -S .sam
however, if you did want to make selections from the sam:

samtools view -S .sam chr1:0-1000000
will grab reads that meet the criteria of being on chr1 between 0 and 1000000 (inclusive)

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