Squid on bacterial genomes about squid HOT 5 CLOSED

SQUID should be able to do that on bacteria, except that it assumes linear genome instead of circular one. Extra post-processing to remove the predictions that connect the end of genome to the beginning may be needed.

In terms of the error, would it be possible for you to share the input files? Without them, it is hard to track down the error.

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With your alignment, you shouldn't use STAR version, since mapping quanlity in STAR and BWA are encoded differently.

Also, SQUID requires sorted alignment, so please sort your bam file with samtools sort before using SQUID.

Please checkout the newest release of SQUID, it fix bugs regarding one case of reading bam alignment record.

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I just finished re-running Squid on my csorted .bam file and it worked! Thank you very much for your help.
May I suggest to specify the requirement for a coordinate sorted bam as an input in the documentation? I know it is common practice but it could be helpful and does not appear in the --help or in the github readme.

Thanks again.

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It is a very good point. We updated the github readme page. Thanks for the suggestion.

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