User: Lina F

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Lina F70
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Location:
Boston, MA
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2 days, 23 hours ago
Joined:
2 years, 4 months ago
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Posts by Lina F

<prev • 30 results • page 1 of 3 • next >
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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 9 days ago by Lina F70
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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 9 days ago by Lina F70
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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 5 weeks ago by Lina F70 • updated 5 weeks ago by Pierre Lindenbaum89k
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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 6 weeks ago by Lina F70
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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 6 weeks ago by Lina F70
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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 6 weeks ago by Lina F70 • updated 6 weeks ago by Charles Warden4.6k
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Comment: C: Yeast GTF file needed for RNA-SeQC run
... Ah, this makes sense -- thanks for the help! ...
written 6 weeks ago by Lina F70
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Yeast GTF file needed for RNA-SeQC run
... Hi all, I have some yeast RNAseq data and I would like to run RNA-SeQC to get an overview of the quality of the run. I got both the reference fasta sequence and the GTF file from Ensembl here: # fasta ftp://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cere ...
gtf qc yeast rna-seq rna-seqc written 6 weeks ago by Lina F70 • updated 6 weeks ago by apa@stowers320
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Comment: C: bwa mem: which parameters to tune to improve alignment?
... Thanks for the suggestion! I mapped with STAR, and it got rid of the sharp cutoffs and peaks which were probably splice sites: ![enter image description here][1] [1]: https://s28.postimg.org/wssvvbej1/Screen_Shot_2016_12_20_at_2_59_51_PM.png ...
written 9 weeks ago by Lina F70
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bwa mem: which parameters to tune to improve alignment?
... Hi all, I have a handful of genes of interest that I am trying to identify in a plant transcriptome dataset. I used bwa mem to map the paired-end transcriptome reads against a reference dataset generated from the genes of interest. The gene sequences I used as leads are not the same organism as t ...
parameters tuning bwa written 9 weeks ago by Lina F70

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