User: michael.ante
michael.ante • 2.9k
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Posts by michael.ante
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Comment:
C: Problem in running STAR
... You allocate 31GB memory, but have only 30.5GB free.
You should stop other processes occupying Memory. ...
written 1 day ago by
michael.ante • 2.9k
1
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1
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95
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Comment:
C: Problem in running STAR
... There is a similar error on [STAR's github][1]. Do you have enough memory available?
cat /proc/meminfo
[1]: https://github.com/alexdobin/STAR/issues/28 ...
written 1 day ago by
michael.ante • 2.9k
1
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1
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87
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... It has a [paper][1] linked, is the assembly/annotation mentioned there?
(I cannot access it, due to paywall)
[1]: http://science.sciencemag.org/content/362/6419/eaav2621 ...
written 3 days ago by
michael.ante • 2.9k
3
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87
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... But you get the names and sizes of the chromosomes. ...
written 3 days ago by
michael.ante • 2.9k
0
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48
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... In case you have varying read lengths , you can also use `--outFilterMismatchNoverLmax`:
> int: alignment will be output only if its ratio of mismatches to
> *mapped* length is less than this value ...
written 5 days ago by
michael.ante • 2.9k
0
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1
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145
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... Have you generated a custom genome with the reference file and its index? ...
written 4 weeks ago by
michael.ante • 2.9k
0
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1
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139
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1
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... Hi GusiG,
The RSeQC too tells you that 96% of your reads cannot be used for inferring the strandedness. This could either be due to the case that 96% of your reads are derived from overlapping gene regions, or due to discrepancies in your annotation.
To check the first idea, just have a look at h ...
written 4 weeks ago by
michael.ante • 2.9k
1
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1
answer
199
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... BBDuk is doing fine. The barcode is in the read id line:
@ST-E00161:..... 1:N:0:TAAGGCGA
BBDuk used according to your output barcodefilter=t ; the number of input reads are equal to the number of output reads. Therefore, you should not have a barcode contamination. ...
written 5 weeks ago by
michael.ante • 2.9k
0
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1
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194
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... This p-value indicates if the differences in number of reads spanning a certain junction are likely to be a "true" difference due to the condition or merely random.
Using this approach would give a p-value for each fusion/recombination event, like in a differential expression analysis. I thought t ...
written 5 weeks ago by
michael.ante • 2.9k
0
votes
1
answer
194
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1
answers
... For the Fisher's exact test, you need to have counts. The normalisation is given by the background data. In your case it could be the total numbers of splice-reads in the 170 kbp area.
...
written 5 weeks ago by
michael.ante • 2.9k
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For A: questions on rna-seq data analysis
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For A: questions on rna-seq data analysis
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For A: questions on rna-seq data analysis
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For A: questions on rna-seq data analysis
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For A: questions on rna-seq data analysis
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For A: questions on rna-seq data analysis
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11 months ago,
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For C: Merge 2 files based on rs number but keep all info only from the first file
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12 months ago,
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For C: Merge 2 files based on rs number but keep all info only from the first file
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13 months ago,
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For A: questions on rna-seq data analysis
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13 months ago,
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