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ChaissonLab/hmcnc 17

Hidden Markov Model based Copy number caller

derekwbarnett/bioconda-recipes 0

Conda recipes for the bioconda channel.

issue commentPacificBiosciences/pbbioconda

Extracting subreads from PacBio BAM using CCS ZMW name

No, any order is fine. Duplicates are ok too. Just has to be one per line.

gevro

comment created time in 3 months

issue commentPacificBiosciences/pbbioconda

Extracting subreads from PacBio BAM using CCS ZMW name

Just a headsup, the input BAM needs a *.pbi index file for this tool. But yeah, this is blazing fast compared to bamsieve, haha

gevro

comment created time in 3 months

issue commentPacificBiosciences/pbbioconda

Extracting subreads from PacBio BAM using CCS ZMW name

We have a tool just for this in bioconda - "zmwfilter" (available for linux-only)

$ zmwfilter --include <zmws.txt> <in.bam> <out.bam> "zmws.txt" should be contain one ZMW ID number per line.

If you only have the full read names, you can extract these with: $ cut -f 2 -d '/' read_names.txt > zmws.txt

gevro

comment created time in 3 months

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