User: michael.ante

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michael.ante2.9k
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Posts by michael.ante

<prev • 315 results • page 1 of 32 • next >
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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.ante2.9k
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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.ante2.9k
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Comment: C: Finding out assembly reference from bam file
... 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.ante2.9k
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Comment: C: Finding out assembly reference from bam file
... But you get the names and sizes of the chromosomes. ...
written 3 days ago by michael.ante2.9k
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Comment: C: Will the --outfiltermismatchNmax in the STAR works for the single end reads?
... 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.ante2.9k
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Comment: C: IGV ignoring indexed and sorted .bai file and trying to create a .fai file to vi
... Have you generated a custom genome with the reference file and its index? ...
written 4 weeks ago by michael.ante2.9k
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Answer: A: Infer experiment - Failed to determine strandin paired end stranded RNA-seq
... 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.ante2.9k
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Comment: C: BBDuk.sh and BBDuk2.sh barcodefilter does not filter the reads
... 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.ante2.9k
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Comment: C: STAR Splice Junctions normalization
... 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.ante2.9k
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Comment: C: STAR Splice Junctions normalization
... 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.ante2.9k

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Commentator 3 days ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
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Scholar 7 weeks ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
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Scholar 8 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
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Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Scholar 13 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
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