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Suppose I have a sam file?
Can I use samtools command to get whole genome data?
Thanks.
Can I use samtools command to get whole genome data?
Thanks.
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Could you describe what "whole genome data" means? -
If we use samtools, we can select chromosome.
The entire means from chr1 to chr 23.Comment
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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.Comment
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Can we identify the start and the end position?
I just guess that start from 0 and end with a big number.Comment
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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.Last edited by dpryan; 11-09-2011, 02:13 PM. Reason: I should really proof read before hitting post...Comment
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to get everything just:
to get everything and the header:Code:samtools view .bam
for .sam, add the sam optionCode:samtools view -h .bam
however, if you did want to make selections from the sam:Code:samtools view -S .sam
will grab reads that meet the criteria of being on chr1 between 0 and 1000000 (inclusive)Code:samtools view -S .sam chr1:0-1000000
Last edited by jbrwn; 11-09-2011, 02:24 PM.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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