User: blur
blur • 110
- Reputation:
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- European Union
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- 3 months, 2 weeks ago
- Joined:
- 4 years, 10 months ago
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Posts by blur
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... as I wrote in my post, none of these appear to have the information I require
gtRNAdb specifically states it does not include NUMTs, the other two as far as I can see have no genomic locations, ...
written 3 months ago by
blur • 110
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... Hi,
I am looking for genomic locations of tRNAs. It's not in gtRNAdb, mitotRNAdb (no genomic locations). I also didn't see it in gencode and a google search didn't help. Any ideas what I can do?
Specifically I need human and mouse.
Thanks! ...
written 3 months ago by
blur • 110
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... thanks! that's great :) ...
written 4 months ago by
blur • 110
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... Hi,
I am looking for a database of small RNAs (snoRNAs, snRNAs, mirs) in plant genomes. Does anyone know of such a DB? I know there are such DBs for human small RNAs.
I know mirbase and mirtarbase, but looking for other small RNAs (preferably bed files of genomic locations if anyone knows where to ...
written 4 months ago by
blur • 110
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... Thanks, I'll try it all
(the library is after experimental rRNA depletion, but I guess it never hurts to check again) ...
written 8 months ago by
blur • 110
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... Hi,
I want to know whether I have DNA contamination in my RNA-seq data.
I have a library with DNAse and one without DNAse and another pair with additional treatment
[DNAse(+) vs. DNAse(-), DNAse(+)+X vs. DNAse(-)+X]
I tried:
1) Checking overall alignment rate of DNAse(+) vs. DNAse(-) and DNAse(+ ...
written 8 months ago by
blur • 110
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... I do think there was a sequencing problem...
I will try and clean it using the tools suggested
Thanks ...
written 8 months ago by
blur • 110
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... There is phiX, but it can't be the reason as all the runs have phiX...
Also, the quality is clearly affected as the errors bars of the reads are very, very long ...
written 8 months ago by
blur • 110
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... Hi,
I have been looking at a library run in Hiseq using fastQC.
Usually I get good Per tile sequence quality, with the entire area looking bluish (OK quality throughout).
But this time I get tiles that appear to give consistently low quality reads over the entire read sequence.
The thing is - I tho ...
written 8 months ago by
blur • 110
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