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Popular Question to
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Answer: Repeated measures design matrix controlling for covariates age and sex
by
Gordon Smyth
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3.4k
> I want to account for sex and age effect
Paired analyses already completely control for all subject-specific characteristics including a…
Comment: orient flipped reads - adapter ligation
by
GenoMax
107k
If you had noticed I had said `selected.fq` to only choose reads you want to RC. You can get those reads by using another tool `bbduk.sh` i…
Comment: Weird error from BWA and BOWTIE2
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SkyL
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thanks, we run `fastQValidator` on the simulator data and found that there are a lot `repeated sequenced identifier`:
```
ERROR on Line 19…
Comment: orient flipped reads - adapter ligation
by
PhilippFW
•
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Thanks for your quick reply, GenoMax.
Your solution would flip all reads, correct? How can I only select those that are in the wrong ori…
Comment: orient flipped reads - adapter ligation
by
GenoMax
107k
> How do I flip/reverse complement reads which have the 'wrong'
> orientation
Using `reformat.sh` from [BBMap suite][1]:
reformat.sh …
Comment: Beginner problem: install python3.7.12 but py_available() still return FALSE
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Sashu
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I see! Thanks for your reminder!
Comment: Beginner problem: install python3.7.12 but py_available() still return FALSE
by
Sashu
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I finally understand what you mean! I paid too much attention on the second sentence but ignored the error information. Thanks a lot!
Comment: Low mapping rate of 10X scATAC-seq reads
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Which aligner are you using? I suggest that you take a few data reads and try doing a blast at NCBI to verify that something untoward has n…
Comment: Splice aware vs splice unaware aligners?
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might be indeed, though I think that is rather a side-effect/consequence of the former rather than a 'goal' .
Most of the times (and this …
Comment: Importing multiple datasets into one folder
by
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Are you interested in moving all `.fastq` files from various folders into one? Because that can be done with a single command, but not sure…
Comment: Beginner problem: install python3.7.12 but py_available() still return FALSE
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Ram
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Please do not delete the post after it has received feedback.
Comment: How can I know the BLAST percentage from kraken2 files ?
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You can't.
In no moment whatsoever Kraken2 performs an alignment. Morever, BLAST is BLAST, Kraken2 is Kraken2, they are not related and p…
Comment: Importing multiple datasets into one folder
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Galaxy specific questions are best asked on their dedicated support forum: https://help.galaxyproject.org/
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Since all cells shed [** free DNA**][1] that circulates (`cfDNA`) (including tumor cells) I don't know if there needs to be a separate data…
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There is actually, well, a sort of citation off the top of my head. Please see the PLINK documentation (section '*Outlier detection diagnos…
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