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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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Unique alignment #5

Closed buyejue closed 7 years ago

buyejue commented 8 years ago

If I want allowed random mapping of reads with multiple genomic hits, is there an argument I should supply directly to Bowtie2 (via BS Seeker 2's command line option) ?

Thanks.

guoweilong commented 8 years ago

BS-Seeker2 does report reads which have multiple genomic hits. You can specific parameter "-M" for bs_seeker2-align.py to save the reads information.

However, the information about multiple alignments (where they could be aligned) are not reported, as being discarded when reporting unique best hit.

Best, Weilong Guo

At 2016-04-26 19:12:47, "buyejue" notifications@github.com wrote:

If I want allowed random mapping of reads with multiple genomic hits, is there an argument I should supply directly to Bowtie2 (via BS Seeker 2's command line option) ?

Thanks.

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