Admin: genomax
genomax ♦ 85k
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Posts by genomax
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Comment:
C: cellranger count help
... If this is 10x data then one of the smaller files (should be re-named `R1`) will contain `cell barcodes+UMI`. Other small file should have Illumina indexes (should be re-named `I1`). Final file should have the actual read data (largest, should be re-named as `R2`).
If you post the SRR# I can take a ...
written 7 hours ago by
genomax ♦ 85k
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... Don't set an auto-delete time, if you were doing that.
BTW: Data looks reasonable. If the adapters are gone then you can try doing the assembly. ...
written 11 hours ago by
genomax ♦ 85k
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... And that is what may happen. I am sure NCBI does not want to spend umpteenth compute cycles reprocessing data. ...
written 12 hours ago by
genomax ♦ 85k
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... From blog link:
> Using 2 quality bins (i.e. good/bad) gives a dramatic improvement over
> no-quality, though the result is not as good as 8-binning.
2 quality bins is closest to the proposal of NCBI that is keeping only 1 bin.
...
written 12 hours ago by
genomax ♦ 85k
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... The images still appear to be broken. Please post correct links. ...
written 13 hours ago by
genomax ♦ 85k
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... I am going to take the liberty of posting a section from [NCBI proposal][1] below that describes the actual process of quality conversion so people can read it right here.
While this may appear like a drastic change, Illumina has been doing something similar for a while by producing [binned Q-scor ...
written 13 hours ago by
genomax ♦ 85k
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... This is something you could have easily found by doing a simple search. Here is the [first result][1].
From [GATK][2]:
> The GRCh38 analysis sets also include a contig to siphon off reads
> corresponding to the Epstein-Barr virus sequence as well as decoy
> contigs. The EBV contig can hel ...
written 15 hours ago by
genomax ♦ 85k
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... > 1- So, how can I improve these results using galaxy tools, in which I
> can move to the assembly step
I don't know if you can provide custom sequences to trimmomatic via galaxy interface. But that would be the way to go to tackle.
>Nextra Transposase sequences
I suggest that you use ...
written 15 hours ago by
genomax ♦ 85k
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... https://panglaodb.se/markers.html ...
written 1 day ago by
genomax ♦ 85k
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Comment:
C: HOMER load genomes not working
... Did you properly install the package following directions? Looks like there are more than one `.pl` scripts and they need to be available in your `$PATH`. You could find the directory that contains those scripts and then add it to your `$PATH` by doing `export PATH=$PATH:/dir_w_perl_scripts` and the ...
written 1 day ago by
genomax ♦ 85k
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