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tommyau / bamclipper

Remove primer sequence from BAM alignments by soft-clipping
MIT License
31 stars 10 forks source link

manifest to bedpe script #1

Closed rjsicko closed 7 years ago

rjsicko commented 7 years ago

Thanks for this program! This is exactly what I am looking for to replicate MSR analysis using bcbio-nextgen. Do you have a script to convert a TruSight/TruSeq manifest file into primer bedpe file? I'm trying to replicate the bedpe in the example folder by manual manipulation and I'm getting slightly different internal end1 & start2's.

tommyau commented 7 years ago

Please refer to the Perl script ./scripts/manifest2bedpe.pl in the latest commit 80eee02a9fe2f59e8669b77ae8502051724ea667. For example, ./scripts/manifest2bedpe.pl < TruSight-Myeloid-Manifest.txt > trusight_myeloid.bedpe

rjsicko commented 7 years ago

thank you very much!

garrulus-glandarius commented 6 years ago

Thank you for the helpful script!