User: adam.faranda

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adam.faranda80
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Posts by adam.faranda

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How to Interpret FDR-TPR (or FDP-TPR) Curves
... I've seen this type of curve now in several papers benchmarking RNA-Sequencing methods. While they look similar to an ROC curve. There are some cases where the curve takes on an unusual trajectory. ![TPR-FDP Curve][1] Image from:[Van den berge K, Perraudeau F, Soneson C, et al. Observation weig ...
rna-seq written 8 weeks ago by adam.faranda80 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: RSEM Error - rsem-calculate-expression
... There are a couple of things I can think of. Check your reference directory ../ref/mouse_125; was this file generated when you built the reference? Also -- which aligner are you using, Bowtie/TopHat or STAR ? ...
written 8 weeks ago by adam.faranda80
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Answer: A: HISAT2 Error Building Index
... It turns out the server that I am working on has a Hard Drive Quota of 231 gigabytes per user. I was very close to this quota (226 Gb) in my home directory. I liberated ~ 37Gb of space by deleting some old files, and the indexer now seems to be working properly. I think that the solution here is: ...
written 9 weeks ago by adam.faranda80
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Comment: C: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... Hi Ana; that is more or less what I am doing. From what I can tell this pipeline is generally considered valid and well accepted. In some pipelines there is a trimming step after running quality control, before running alignments. I've found this to have relatively little impact on my data, but m ...
written 9 weeks ago by adam.faranda80
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Answer: A: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... I have been using FastQC from the Babraham institute. It is easy to use and gives fairly comprehensive summary statistics. Its output is compatible with multiqc. Multiqc can be used to aggregate several qc reports into a single unified document. FastQC: [https://www.bioinformatics.babraham.ac.uk ...
written 9 weeks ago by adam.faranda80
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HISAT2 Error Building Index
... I consistently get the following error message when I try and build a HISAT2 index for a Mouse geneome. Error: Encountered internal HISAT2 exception (#1) My call to hisat2 is as follows: hisat2-build -f -p 8 --ss genome.ss --exon genome.exon $GENOME genome_tran Where "$GENOME" contains ...
rna-seq hisat2 written 9 weeks ago by adam.faranda80
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What impact does sorting by read name have on RSEM abundance estimates
... The RSEM utility "rsem-calculate-expression" has a setting "--sort-bam-by-read-name". The documentation states that doing so will result in deterministic maximum likelihood estimates, at the cost of longer run-times and larger memory requirements. By default, this setting is disabled Given the sa ...
tools rna-seq rsem written 10 weeks ago by adam.faranda80
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Comment: C: STAR-RSEM RNA-seq pipeline is deterministic?
... RSEM has a setting "--sort-bam-by-read-name" which according to the authors will provide deterministic "maximum-likelihood" estimates from independent runs. It is disabled by default. [http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html][1] [1]: http://deweylab.biostat.wisc.e ...
written 10 weeks ago by adam.faranda80
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Duplicates in Biomart Query, Ensembl ID maps to multiple Entrez genes.
... When I run the following query on "ENSMUSG00000001175", I retrieve records for 2 corresponding entrezgene_id's (Calm1 and Calm2). The first record is correct, however the second record, "12314" is actually Calm2. annot<-getBM( attributes = c( "ensembl_gene_id", "entrezgene_i ...
ncbi ensembl biomart written 5 months ago by adam.faranda80 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: PCA on RNAseq time series data
... Hi @swbarnes2 -- I'm working on a similar type of project as the OP; but I still have a lot to learn about mitigating batch effects. If you include the batch covariate as a factor in the model design matrix, is that sufficient? I'm also wondering how you might apply to cluster analysis. Is there a ...
written 5 months ago by adam.faranda80

Latest awards to adam.faranda

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
Scholar 9 months ago, created an answer that has been accepted. For A: Mysterious genes in my Biomart results (genes that were not part of original que

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