Hi Nandini, We suggest that you contact the mailing list for samtools:
https://lists.sourceforge.net/lists/listinfo/samtools-help Hopefully they will be able to help you. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Nandini B <[email protected]> Date: Thu, Aug 4, 2011 at 2:01 AM Subject: [Genome] samtools flagstat To: [email protected] Hello, I am trying to use the samtools flagstat in order to generate the statistics. The bam files are generated from bioscope and here's what i get samtools flagstat myFile.bam > myFile.stats 3706062915 + 0 in total (QC-passed reads + QC-failed reads) 1284337071 + 0 duplicates 3706062915 + 0 mapped (100.00%:nan%) 2988908908 + 0 paired in sequencing 1480626898 + 0 read1 1508282010 + 0 read2 1978289514 + 0 properly paired (66.19%:nan%) 2539279046 + 0 with itself and mate mapped 449629862 + 0 singletons (15.04%:nan%) 476297856 + 0 with mate mapped to a different chr 209157066 + 0 with mate mapped to a different chr (mapQ>=5) Is this output in the right format ?? Is something wrong with my input file ? Thank you, Regards, Nandini _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
