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inconsistent between .fq.gz and .fastq? #4
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Dear @AMChalkie, The current version does not support gzipped FASTQ file, so you need to unzip the files. But the suggestion will be great for the CB^2. I will start to add the function soon. Thank you, Hyun-Hwan Jeong |
@AMChalkie, the current github version supports gzipped FASTQ files. I wonder you are willing to test the version and let me know if you have any problem with that. Thank you! Hyun-Hwan Jeong |
Yes that works fine now. I notice that mappability information is not printed during the process now, which I thought was a good feature previously. |
@AMChalkie you should see the message if you set the Thank you, Hyun-Hwan Jeong |
@AMChalkie, Can you test on it again? The version which you tested has an incompatibility issue with Windows OS. So, I made some changes and wonder the change doesn't cause any problem. Thank you, Hyun-Hwan Jeong |
Edit: Started with a fresh R environment and I can't reproduce this behavior. I suspect it was an environment path issue not a CB2 issue. Sorry for the false alarm. |
Not a problem, and as you figured out, it has to support both - since CB2 clarifies whether it is gzipped by checking file names' suffix: https://github.com/LiuzLab/CB2/blob/57d7fd5548c162b175a9dc6f5a57f1f73822eb0d/R/helpers.R#L69 |
Strange as this may sound, I get different results when using a .fq.gz vs a .fastq file (when the .fastq is a zcat of original). I get different mappability results (0.018 ish vs the expected 85%).
Would be great if this was handled automatically and input from .fq.gz was handled correctly, or alternatively at least a warning that this might be what's happening.
Otherwise - very useful software thank you!
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