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khyox avatar khyox commented on August 15, 2024

Hi @fancyge, thanks for the enhancement suggestion. For processing kraken output you have already the option to taking compressed files (see Kraken: use of compressed files). Which output files are you thinking of? Thanks.

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fancyge avatar fancyge commented on August 15, 2024

Hi, thanks a lot for the quick response! I have already got the centrifuge classification files and want to run rextract to filter the reads. I noticed that rextract can only take fastq file but will go wrong with "fastq.gz" file. I prefer "fastq.gz" for storage saving purpose.

Thank you.

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khyox avatar khyox commented on August 15, 2024

OK, I see, it is about rextract. The issue #28 is also an enhancement suggestion, so I will probably address both of them soon.

About the -i option, you have to prepend any taxid to include with such a flag. In your case:

rextract -f my_classification_results.txt multiple -i 9606 -i 452 -1 R1.fq -2 R2.fq

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fancyge avatar fancyge commented on August 15, 2024

Thanks! Hope to see it soon! Quite useful tools!
By the way, do you have an idea what score (-y) I should feed to rextract for filtering centrifuge results? I have 150bp fastq files from illumina sequencing.

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fancyge avatar fancyge commented on August 15, 2024

I just added some commands to make it possible to take&output zipped fastq files. It might not be ideal but can be used at the moment. Thanks.

rextract.py.zip

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khyox avatar khyox commented on August 15, 2024

By the way, do you have an idea what score (-y) I should feed to rextract for filtering centrifuge results? I have 150bp fastq files from illumina sequencing.

My recommendation is to avoid too low minscore (-y flag also) values to filter sequences with low scores. Also, if you have control sequences, you may want to lower ctrlminscore (-z flag also) to have more sequences in the controls and thus more sequences removed after the robust control removal algorithm. So, --minscore 35 and --ctrlminscore 25 could be good values to start with.

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khyox avatar khyox commented on August 15, 2024

I just added some commands to make it possible to take&output zipped fastq files. It might not be ideal but can be used at the moment. Thanks.

rextract.py.zip

Thanks! If you open a PR I'd happy to check it and include it in the master branch.

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