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peterjc / pico_galaxy

Galaxy tools and wrappers for sequence analysis
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How about the PE reads from sample_seqs.py #16

Closed yifangt closed 7 years ago

yifangt commented 8 years ago

I was wondering how your sample_seqs.py deals with PE reads to keep the "read-pair" while sampling. Do the PE reads have to be interleaved? Thanks!

peterjc commented 8 years ago

If you have interleaved paired reads, just tick the "Interleaved paired reads" option. Then you can get e.g. every 100th pair.

If you have two matching files, run the tool twice on both with the same settings (e.g. every 100th read), and you'll get two matching smaller files. Maybe I need to make the example in the help text more explicit?

yifangt commented 8 years ago

Thanks! "Maybe I need to make the example in the help text more explicit?" --Not really, at first sight I was thinking your script will take two files for PE reads, and I did not realized "running twice" will do the trick. Thanks a lot!