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I mean, how do I see if two reads come from the same sample? The manual only tells me that 2 reads having identical QNAME are paired-end, right? Could someone tell how to read QNAME, above all it's such a long string of words that must tell something other than that...
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I just wanted to know if there's barcode for sample information (in cases of pooled sample), where would it be? Thx~~ -
What manual?Comment
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Often the QNAME is info about the instrument and the date of run, and the lane and tile and xy coordinates. The read group might tell you the sample name. That might be stored in an NM tag in the .sam file, or in the @RG header of the .sam fileComment
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The NM tag is for the # of mismatches. Look in the RG header, if present.Originally posted by swbarnes2 View PostComment
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Right, typo on my part. The SM tag might contain a sample name.Originally posted by nilshomer View PostComment
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Well, the description for the SM tag is"SM:Sample. Use pool name where a pool is being sequenced." I wasn''t putting it clearly...what I meant was, if this sample is pooled, and the origins of the sample content each is barcoded, is it possible that this infomation is contained in .SAM format? And this must be contained in the non-header sectoin...Originally posted by swbarnes2 View Post
If it is not, how is that usually done? Is it customary that I ligate an adaptor to each sample origin, pool them, sequence, and look at the beginning of each read to see which origin of sample it came from?
Lots of thx!!!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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