I used two aligners for paired end reads, and got two sam files. Are there any ware or scripts to implement these two operations?
- How to find the intersect of two sam files by read ids? To use bedtools, one needs to convert sam to bam to bed and work on 2 bed files.
- I'd like to merge the 2 sam files and, for duplicated reads being aligned in both, select a better alignment by the number of mismatch (NM).
Please advise.
- How to find the intersect of two sam files by read ids? To use bedtools, one needs to convert sam to bam to bed and work on 2 bed files.
- I'd like to merge the 2 sam files and, for duplicated reads being aligned in both, select a better alignment by the number of mismatch (NM).
Please advise.
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