[BioC] loss of stranding in alignments from recent versions of Rsubread

[Wei Shi]

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] Œ1.10.1‚
> 
> -- 
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
> 
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> 
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