User: Lina F

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Lina F80
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2 years, 5 months ago
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Posts by Lina F

<prev • 33 results • page 1 of 4 • next >
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Comment: C: How to assess biases in ribosomally depleted RNAseq data?
... Could you elaborate on how to correlate the data? I plotted three samples below that were treated with three different rRNA depletion protocols. The third protocol removed the most rRNA (i.e. the percentage value on the 2nd y-axis is highest). ![enter image description here][1] ![enter image desc ...
written 9 days ago by Lina F80
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Comment: C: How to assess biases in ribosomally depleted RNAseq data?
... Yes I have. I ran SortMeRNA to remove ribosomal RNA reads before quantifying with sailfish. This is ecoli data, in case it matters. ...
written 21 days ago by Lina F80
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How to assess biases in ribosomally depleted RNAseq data?
... Hi all, I am interested in evaluating four different ribosomal depletion wet lab protocols and I want to see if any of them are biased against transcripts other than rRNA. Ultimately, I want to find out which of the protocols is the least biased towards other transcripts. I quantified all the samp ...
bias rna-seq transcripts written 21 days ago by Lina F80
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Answer: A: RSeQC GeneBody function error. Stops at R Script Step
... Usually, the "null device 1" line means that R did open the device for drawing. Did you check that the pdf file was not created? Also, if you don't set up your output prefix option correctly, the file might start with a period, which makes it look invisibe to a Linux or Mac OSX terminal. So if y ...
written 5 weeks ago by Lina F80
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How does RNA-SeQC calculate the "Mean CV" value?
... I took a look at the journal article and it specifies: **Mean coefficient of variation: the mean coefficient of variation across all transcripts.** Source: https://doi.org/10.1093/bioinformatics/bts196 Note that I wasn't able to actually look at the supplementary data since the link in the articl ...
coefficient of variation qc rna-seq written 5 weeks ago by Lina F80
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How to format input data for Picard CollectRnaSeqMetrics
... Hi all, I am trying to run Picard's CollectRnaSeqMetrics tool and noticed that my output contains a lot of zero values. I only get values for the following fields: PF_BASES -------------> 553934269 PF_ALIGNED_BASES -----> 552090508 RIBOSOMAL_BASES ------> 6920715 INTERGEN ...
gtf picard rna-seq written 9 weeks ago by Lina F80 • updated 9 weeks ago by Pierre Lindenbaum91k
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Comment: C: RNA-SeQC does not calculate information about "Strand Specificity"
... Thanks for the suggestion! I am actually using the [RNA-SeQC][1] tool from the Broad Institute; that's where the report came from. I will take a look at the tool you mentioned, maybe it will be more appropriate. [1]: http://archive.broadinstitute.org/cancer/cga/rna-seqc ...
written 10 weeks ago by Lina F80
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Answer: A: Classification of bacteria - bioinformatics
... I don't know if there is an easy ready-made answer for this question, but KEGG has a rudimentary "tree" of sorts: http://www.genome.jp/kegg/catalog/org_list.html You could download this html file and parse it and it will give you the links to genbank. Maybe Python's [beautifulsoup][1] module can h ...
written 10 weeks ago by Lina F80
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RNA-SeQC does not calculate information about "Strand Specificity"
... Hi all, I recently ran RNA-SeQC on yeast RNAseq data to assess the quality of the sequencing run. Unfortunately, the tool returned only "NA" for the "Strand Specificity" section: ![rnaseqc_strand_specificity_output][1] This sample contains single-end reads that I mapped to the reference using ST ...
qc rna-seq written 10 weeks ago by Lina F80 • updated 10 weeks ago by Charles Warden4.7k
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Comment: C: Yeast GTF file needed for RNA-SeQC run
... Ah, this makes sense -- thanks for the help! ...
written 10 weeks ago by Lina F80

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