User: adam.faranda
adam.faranda • 80
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Posts by adam.faranda
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... 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 ...
written 8 weeks ago by
adam.faranda • 80
• updated
7 weeks ago by
Biostar ♦♦ 20
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... 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.faranda • 80
1
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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.faranda • 80
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... 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.faranda • 80
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... 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.faranda • 80
1
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... 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 ...
written 9 weeks ago by
adam.faranda • 80
1
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... 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 ...
written 10 weeks ago by
adam.faranda • 80
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... 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.faranda • 80
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... 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 ...
written 5 months ago by
adam.faranda • 80
• updated
4 months ago by
Biostar ♦♦ 20
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3
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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.faranda • 80
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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