User: cschu181

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Posts by cschu181

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Comment: C: output path issue on Busco (python)
... Have the script generate/modify the config.ini. ...
written 3 days ago by cschu1811.4k
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Comment: C: Error in transferring annotations to a new assembly using RATT
... I am using mummer-4.0.0beta2/mummer3.23 (the latter one installed with conda) and it works for me. Maybe include the commented out mummer-addition to the path and export the path to see how that goes. Just because PAGIT brings its own mummer it doesn't necessarily add it to the path (although I migh ...
written 11 days ago by cschu1811.4k
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Comment: C: Error in transferring annotations to a new assembly using RATT
... 1) Ok, was worth a try. 2) Yes, I meant that version. Since that doesn't work I'll agree with Lieven Sterck about the potential nucmer issue. 3) This is probably not related to your issue, but this is what you have to change in `main.ratt.pl`: 229c229 < if (defined(@{$$ref_shift{$ref ...
written 11 days ago by cschu1811.4k
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Comment: C: Error in transferring annotations to a new assembly using RATT
... Don't you need to export PATH after modifying it? Another thing: have you tried the standalone version of RATT? That one works for me with the example. Last: I don't see any sign for this in your output, but the RATT code uses a deprecated feature that is not compatible with more modern Perl insta ...
written 12 days ago by cschu1811.4k
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Comment: C: Learn python programming
... There is no "best" way. You need to find your own. You could do the practical approach and use Python to solve some problem that you're working on (for instance, in my case that was processing of Protein Data Bank data files during my master's work). You could attend a course. https://swcarpentry ...
written 21 days ago by cschu1811.4k
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Answer: C: Extract unmapped reads using RNAME
... From the [SAM specification][1]: > Bit 0x4 is the only reliable place to tell whether the read is unmapped. If 0x4 is set, no assumptions can be made about RNAME, POS, CIGAR, MAPQ, and bits 0x2, 0x100, and 0x800. I.e., no. [1]: https://samtools.github.io/hts-specs/SAMv1.pdf "SAM format spec ...
written 29 days ago by cschu1811.4k
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Comment: C: What's new in CAS9?
... > It's a version, isn't it? No. Cas8 and Cas9 are two different proteins. ...
written 4 weeks ago by cschu1811.4k
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Comment: C: Custom Database Has Spaces
... I don't know... sometimes replacing spaces with underscores is exactly what I seem to be doing all day... ...
written 4 weeks ago by cschu1811.4k
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Comment: C: Paired-end flag for singleton
... The flag does not change. Each mate has its own flag. 89 means (1=paired | 8=mate unmapped | 16=read reverse strand | 64=first in pair) and 133 means (1=paired | 4=unmapped | 128=second in pair). So, if you want to look for singletons that are aligned, use flag 8, if you want the non-aligned mate, ...
written 8 weeks ago by cschu1811.4k
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Comment: C: total beginner trying to learn about quality control
... It does. By default, FastQC creates a directory with text output in addition to the .html. One can choose the --noextract option to keep that directory as a zipped archive. ...
written 9 weeks ago by cschu1811.4k

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