Hello everyone,
I am working with Arabidopsis RNA-seq data and have used HISAT, TOPHAT and STAR aligners that gives a summary statistics showing the percentage of uniquely mapped reads and unmapped reads etc. However, there are some aligners that do not give such statistics e.g. CRAC etc., so the question is:
How can we calculate the percentage of uniquely mapped reads from SAM/BAM file only?
Thank you in advance :)
Dear Zeeshan...
Please, have a look to the link below:
https://www.sciencedirect.com/science/article/pii/S0888754317300204
Best luck
How about bamtools, I have used it several time to compare my bam files with different mappers.
https://github.com/pezmaster31/bamtools
Goog luck
@Ayoob Obaid, Thanks for your reply but in that paper they used simulated reads, usually the simulators create an additional file that can be used for calculating the efficiencies.
@Silvia, thanks for the reply. I am also trying to do similar thing, compare performance of different aligners for my data. Can you be a bit more specific? as there are lot of functions of bamtools.
Hi @Zeeshan
Bamtools stats is the option you could use.
Good luck,
Silvia
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