Tweet
I have a collapsed fasta files with all my counts and the corresponding sequences. I would like to annotate those sequences onto a gff file to find out what they are. Is this possible? Usually I would need a bam/sam file, but I dont have that for these sequences.
-
-
So map the collapsed fasta file to something and then count accordingly. Just make the counts part of the read name so you can get them back later. BTW, you made your life more difficult by collapsing things like that. Aligners are fast enough these days to handle whatever size data you want to throw at them.
-
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
-
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...
Comment