I went to dump some ChIP-seq reads to a BED file using sam2bed, and found that they all had a strand of '*'. Looking into it a bit further, the culprit seemed to be the alignments written to the SAM file, e.g. H9_WYSOCKA_NEURAL.H3K27ac.643 4 * 0 0 * chr1 1 0 GGTAGGCGGAGCTTGCAGTGAGCTGAGATCGCGCCA AA>5A=CA745A%%%%%%%%%%%%%%%%%%%%%%%% H9_WYSOCKA_NEURAL.H3K27ac.644 16 chr3 54404886 199 36M * 0 0 CACTTTAACATTTTTCCTTCAATCTCAGCATTCCTC C>C=@5:@==4=A?=CDBDDD=-D:DCCEECADD5B AS:i:5 NM:i:0 H9_WYSOCKA_NEURAL.H3K27ac.645 0 chr17 7073894 199 36M * 0 0 GTAAACTTGTCTGTTTTCTTATACCTCTAAAATTTT D5?DDC=ABA:@ :=@BCBB8:B=?BBBDBB?:>5@B AS:i:6 NM:i:0 H9_WYSOCKA_NEURAL.H3K27ac.646 4 * 0 0 * chr1 1 0 CAGAGGACGGTACCTGTATTAAATGTATTAGACAGG 3?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% H9_WYSOCKA_NEURAL.H3K27ac.647 4 * 0 0 * chr1 1 0 GTCCCAACCAGAGGCCCTGAGCGGAGGTTCTCGGGG ;7,4>,B<=6C>C:?%%%%%%%%%%%%%%%%%%%%% H9_WYSOCKA_NEURAL.H3K27ac.648 4 * 0 0 * chr1 1 0 ATATTGACAACTGCCGGCAATTGGCATCATCTATCT ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% H9_WYSOCKA_NEURAL.H3K27ac.649 4 * 0 0 * chr1 1 0 TGCATTCTTTTGGAGGAGGAGAGGTGCTCTGCTTTT ADC=ED-=D;=@C5CD,DA4D:DDADBB5?D:D:5> Previously, I didn't have this problem (I went back and checked). So despite my worries that sam2bed was somehow to blame, it was just doing what it was told (although I would like it if proper BED6 output was the default from sam2bed!). This seems to be an alignment issue. Do I need to rebuild my indices for R-3.0/Rsubread 1.10 or some such? Here is what I'm running: Welcome to R version 3.0.0 (2013-04-03) > packageVersion('Rsubread') [1] ‘1.10.1’ -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

Hi Tim, The sam2bed function does not output strand information in both the latest version and old versions of Rsubread. I have just changed it to make it output a BED6 file, which includes strand information for each read. I just committed the changes to bioc devel svn. You should be able to access it in a couple of days. Best regards, Wei On Apr 22, 2013, at 7:58 AM, Tim Triche, Jr. wrote: > I went to dump some ChIP-seq reads to a BED file using sam2bed, and found > that they all had a strand of '*'. Looking into it a bit further, the > culprit seemed to be the alignments written to the SAM file, e.g. > > H9_WYSOCKA_NEURAL.H3K27ac.643 4 * 0 0 * > chr1 1 0 GGTAGGCGGAGCTTGCAGTGAGCTGAGATCGCGCCA > AA>5A=CA745A%%%%%%%%%%%%%%%%%%%%%%%% > H9_WYSOCKA_NEURAL.H3K27ac.644 16 chr3 54404886 199 36M > * 0 0 CACTTTAACATTTTTCCTTCAATCTCAGCATTCCTC > C>C=@5:@==4=A?=CDBDDD=-D:DCCEECADD5B > AS:i:5 NM:i:0 > H9_WYSOCKA_NEURAL.H3K27ac.645 0 chr17 7073894 199 36M * > 0 0 GTAAACTTGTCTGTTTTCTTATACCTCTAAAATTTT D5?DDC=ABA:@ > :=@BCBB8:B=?BBBDBB?:>5 at B AS:i:6 NM:i:0 > H9_WYSOCKA_NEURAL.H3K27ac.646 4 * 0 0 * > chr1 1 0 CAGAGGACGGTACCTGTATTAAATGTATTAGACAGG > 3?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > H9_WYSOCKA_NEURAL.H3K27ac.647 4 * 0 0 * > chr1 1 0 GTCCCAACCAGAGGCCCTGAGCGGAGGTTCTCGGGG > ;7,4>,B<=6C>C:?%%%%%%%%%%%%%%%%%%%%% > H9_WYSOCKA_NEURAL.H3K27ac.648 4 * 0 0 * > chr1 1 0 ATATTGACAACTGCCGGCAATTGGCATCATCTATCT > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > H9_WYSOCKA_NEURAL.H3K27ac.649 4 * 0 0 * > chr1 1 0 TGCATTCTTTTGGAGGAGGAGAGGTGCTCTGCTTTT > ADC=ED-=D;=@C5CD,DA4D:DDADBB5?D:D:5> > > Previously, I didn't have this problem (I went back and checked). So > despite my worries that sam2bed was somehow to blame, it was just doing > what it was told (although I would like it if proper BED6 output was the > default from sam2bed!). This seems to be an alignment issue. > > Do I need to rebuild my indices for R-3.0/Rsubread 1.10 or some such? > > Here is what I'm running: > > Welcome to R version 3.0.0 (2013-04-03) >> packageVersion('Rsubread') > [1] ?1.10.1? > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}