Hello Feliks, > Same issue was reported here https://github.com/jeff-k/resolvepairs > explaining that the error is due to more than one pair of reads having > the same query name.
I would just add that the read name reported in your picard error: > Exception in thread "main" net.sf.picard.PicardException: Illegal > mate state: HWI-ST1006:65:C0VRNACXX:2:1102:15430:43570 looks like the standard Illumina naming scheme, and, to my limited understanding, you should not be finding collisions in read names unless there is a configuration problem upstream. The same caution is noted on the github page you link: "Note that such improperly named reads might indicate a failure in an early stage of the sequencing pipeline" For troubleshooting purposes, it might be useful to grep the BAM/SAM file for the read name in the error and see (a) how many lines are returned, and (b) what the flags tell you about the alignments returned and how many read pairs they represent. Also, regarding your issues with the 'resolvepair' script, the description notes "resolvepair requires SAM input sorted by read name", which I suspect the tophat output is not, so you might try this sort if you haven't done so already. Regards, Jeremy ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
