Bowtie2 currently supports replacing sequence and qual in .SAM output with '*' for secondary alignments via --omit-sec-seq, however it does not support doing so for primary alignments. Support for doing so with primary alignment would be helpful for mapping operations performed by woltka as used in Qiita
Bowtie2 currently supports replacing sequence and qual in .SAM output with '*' for secondary alignments via
--omit-sec-seq, however it does not support doing so for primary alignments. Support for doing so with primary alignment would be helpful for mapping operations performed by woltka as used in Qiitacc @sfiligoi @antgonza @qiyunzhu