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Thanks I'll give that a try.
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It‘s so hard for me to understand those answers.Comment
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Hi All,
I converted the .bam file to .bai file using
$ samtools index test_sorted.bam test_sorted.bai (and now I have both in the same folder). When i upload the .bam file to IGV it seems to work, but i see no alignment of the reads against the genome (i do see the genome in blue)
I am using the TAIR10 genome.
what could be this? ideas?
many thanks
GLast edited by Gonza; 10-17-2014, 09:14 AM.Comment
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Chromosome names need to match between your BAM/genome in IGV (I assume you are using the built-in genome) in order for IGV to be able to display your data. Other possibility is you need to start zooming in/out/sideways depending on the relative location of IGV display, to see the mapped reads.Originally posted by Gonza View PostComment
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Thanks, I just realized that you need to start scrolling to the side to see where the reads are. It wasn't really intuitive....sorry for the silly question.Comment
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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...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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