Hi Siva, I don't really use IGV, so can't really help. The only suggestion I can think of is to make sure the reference IDs in the bam match those in IGV e.g. Does the 'Ha3' reference ID exist in the bams? Cheers,
Chris From: Siva Nandy Date: Tuesday, 19 May 2015 12:20 To: Christian Cole Cc: samtools Subject: Re: [Samtools-help] [E::hts_hopen] samtools index problem >Hi Christian, > >The "$ samtools view less_stringent_Ha412-34CDSHa.sorted.bam" works fine, I >can see the mapping, but for IGV I should have in the repository the >sorted..bam, > .bam and indexed.bam files. >Then I give to IGV the sorted.bam file only. >But got this capture, I can't see the mapping result, only the reference >sequence appears. > >So I thought it's maybe because of an error in my indexed.bam as I can't open >it rightfully with samtools view and because of error messages. > >advance thanks, >Siva > > > > >2015-05-19 13:03 GMT+02:00 Christian Cole (Staff) ><[email protected]>: > >Hi Siva, > >You are trying to open the index file with samtools rather than the bam file. >Try this instead: >$ samtools view less_stringent_Ha412-34CDSHa.sorted.bam > >Same goes for IGV. Point it at the .bam rather than the .bam.bai file. >Regards, > >Chris > > >From: Siva Nandy >Date: Tuesday, 19 May 2015 11:10 >To: samtools >Subject: [Samtools-help] [E::hts_hopen] samtools index problem > > >>Hi everyone, >> >>I've found a lot's of discussion about this problem, but haven't found the >>solution. >>I got this error: >> >>[E::hts_hopen] fail to open file 'less_stringent_Ha412-34CDSHa.sorted.bam.bai' >> >>[E::hts_open] fail to open file 'less_stringent_Ha412-34CDSHa.sorted.bam.bai' >>samtools: failed to open "less_stringent_Ha412-34CDSHa.sorted.bam.bai" for >>reading: Success >> >> >>When I read the sorted.bam file like that: >>-bash-4.1$ samtools view less_stringent_Ha412-34CDSHa.sorted.bam.bai >> >> >>Actually I've done a bwa mapping, and trying to see my mapping results in >>IGV, so need to have sorted and indexed files of bam. >> >>So got these: >> >> >>-rw-rw-r-- 1 nandy inra 124K May 19 10:33 less_stringent_Ha412-34CDSHa.sam >>-rw-rw-r-- 1 nandy inra 174K May 19 11:21 less_stringent_Ha412-34CDSHa.bam >>-rw-rw-r-- 1 nandy inra 18K May 19 11:22 >>less_stringent_Ha412-34CDSHa.sorted.bam >>-rw-rw-r-- 1 nandy inra 559K May 19 11:59 >>less_stringent_Ha412-34CDSHa.sorted.bam.bai >> >> >>But when in IGV I gave the necessary there is no visualisation, so i think >>it's maybe because of this error. >> >>regards, >>Siva > > > >The University of Dundee is a registered Scottish Charity, No: SC015096 > > > The University of Dundee is a registered Scottish Charity, No: SC015096 ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
