Tweet
In a SAM file generated from Bowtie, I found one entry has '*' in the CIGAR field. What does this mean, bad alignment?
Thanks
Thanks
-
-
It means "not available" in the SAM spec. Typically, this happens when the read isn't aligned (RNAME - 3rd field - is also '*' and 0x4 is set in the FLAG field). -
Thanks, arvid.
To what extend, Bowtie sets the FLAG to 0x4 for a read, and make the CIGAR field "not abailable". What are the measure and threshold bowtie uses for setting this?
ThanksComment
-
Well, using the settings (default or your specific choices), Bowtie found no reportable alignment for that read.
It is not possible to make a general statement about this behaviour here as it depends entirely on the settings you provided bowtie with and the nature of your reads and reference. Check the bowtie manual, typically you should look at alignment and reporting modes - these and their sub-options control alignment sensitivity and reporting filters.Comment
-
Hi Arvid,
Thank you very much for the help.Comment
-
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 -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment