Hi Wei, Since this is a bwa error, you might try the bwa mailing list (http://sourceforge.net/p/bio-bwa/mailman/).
Devon ____________________________________________ Devon Ryan, Ph.D. Email: [email protected] Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn, Germany On Jun 6, 2014, at 6:27 PM, Shao, Wei (NIH/NCI) [C] wrote: > Hi, > I have worked on aligning some sequence sets with bwa. I found some very > strange cases. For example, The attached CAGACGGTGA_bad_fastq file cannot be > aligned with bwa mem to get correct SAM file (attached). One sequence is > concatenated with another in this SAM file. However, it can be aligned with > bowtie2 to generate a correct (to me anyway) SAM file. But, either of these > two SAM files cannot be converted to Bam files with the command: > > >samtools view -bS CAGACGGTGA_bowtie.sam > CAGACGGTGA_bowtie.bam > > This is the error message I got: > > [samopen] SAM header is present: 1 sequences. > Parse error at line 4: sequence and quality are inconsistent > Abort (core dumped) > > On the other hand TATAACGGAG files are perfectly OK with either bowtie2 or > bwa. > > Attached are 7 files. Those with CAGCGGTGA prefix are problem files and those > with TATTCGGAG are good ones. Each set has a fastq file and two sam files > from either bowtie2 or bwa. Good_ref.fas is the reference sequence. > > > With best regards, > > > Wei Shao > > <CAGACGGTGA_bad.fastq><CAGACGGTGA_bowtie.sam><CAGACGGTGA_bwa.sam><good_ref.fas><TATAACGGAG_bwa.sam><TATAACGGAG_good.fastq><TATTCGGAG_bowtie.sam>------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech_______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
