User: igor

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igor20
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Posts by igor

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tximeta remote versus local reference files
... BioC 3.8 was just released and there is a great new package tximeta (at least if you work with Salmon). I am still trying to properly understand how it works. The vignette contains the following section: However, to avoid downloading remote GTF files during this vignette, we will point to a GTF fil ...
tximeta written 6 weeks ago by igor20 • updated 6 weeks ago by Michael Love20k
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... Thank you for the explanation. I should've tried more samples. Using the updated example and real samples produces reasonable results. ...
written 6 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... I tried running the example you posted. The result is close to yours: > gsva(normcounts, list(GS1=1:10, GS2=20:30), kcdf="Poisson") Sample1 Sample2 GS1 -0.148823642 0.19004598 GS2 0.002574801 0.04970183 I also tried converting to logCPM values and using the Gaussian kernel: > ...
written 6 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... Thank you for clarifying. Would I also need to length-normalize (convert to TPMs/FPKMs) if I use the Gaussian kernel? Or would normalized counts be appropriate? ...
written 6 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... There is a recent related thread on the GenePattern forum: You can run ssGSEA using RNA-Seq data. This would generally work if your samples raw counts are not too different from one another. If counts vary too much, you may consider normalizing your data (e.g., so that they are between 0 and 1). Ad ...
written 6 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... When you say "integer counts", do you mean that they have to be the raw counts or can they be normalized counts (wouldn't be integers)? ...
written 6 months ago by igor20
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Rsamtools insert size
... I am using Rsamtools to scan a BAM file generated with Bowtie2 (local alignment mode). I am interested in the insert sizes. Most of the time, everything works as expected. However, I noticed an issue with soft-clipped reads. If the fragment is smaller than read length and the reads go past the start ...
rsamtools bam samtools bowtie2 written 10 months ago by igor20
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Comment: C: listDatasets(ensembl) displays strange behavior + scerevisiae_gene_ensembl not a
... I am also having the same problem with listDatasets() returning a different output every time. Very strange behavior. ...
written 12 months ago by igor20
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Counting exonic reads with DEXSeq and GenomicAlignments
... The DEXSeq vignette describes several protocols for obtaining exon counts. One option is to use the dexseq_count.py script (powered by htseq) that comes with the package. Another option is to use summarizeOverlaps directly in R. I tried both methods with unstranded parameters and the results were id ...
dexseq genomicalignments exon usage written 14 months ago by igor20
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Comment: C: DESeq: large difference in number of replicates per condition
... I would add that you should also pay attention to outlier filtering/replacement (see DESeq minReplicatesForReplace) if you expect your large group to be heterogenous. I've seen people run into trouble with that when handling large groups. ...
written 14 months ago by igor20

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Popular Question 3 months ago, created a question with more than 1,000 views. For DESeq2 with many samples
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Popular Question 17 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
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