User: igor

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igor20
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United States
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3 years, 5 months ago
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Posts by igor

<prev • 65 results • page 1 of 7 • next >
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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 3 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 5 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 7 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 7 months ago by igor20
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Comment: C: How to normalize Microarray expression data?
... Although the question says "Affymetrix SNP 6.0 data", it also says "Microarray expression Data". Thus, it may very well be an expression array, not a SNP array. Then gene symbols would make sense. ...
written 7 months ago by igor20
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minfi estimateCellCounts normalized beta values adjusted for cell type
... There is an estimateCellCounts() function in minfi. One of the parameters is returnAll which returns normalized user supplied data. That is returning quantile-normalized values that were normalized along with the reference dataset. Is there a way to get values adjusted by cell-type composition? The ...
minfi 450k written 11 months ago by igor20
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Comment: C: DiffBind matrix of values
... I am using DESeq2-based analysis, so thanks for clarifying that part. I guess DBA_SCORE_RPKM should be close enough (or as close as possible) for something like plotting. Is there a chance DESeq2 normalization becomes an option at some point? If you are just using plain DESeq2, they provide an opti ...
written 20 months ago by igor20
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DiffBind matrix of values
... I am using DiffBind and trying to export the matrix of values for all peaks. If I use dba.report() with bcounts=TRUE, I get those values, but it's only for the two groups being compared. What if you have more than two groups? I tried dba.peakset() with bRetrieve=TRUE. That seems to return what I wa ...
diffbind written 20 months ago by igor20 • updated 20 months ago by Rory Stark2.4k
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DiffBind for ATAC-seq
... Normally, DiffBind is used for ChIP-seq data, but I've seen it used for ATAC-seq as well. I don't see any issues with that. MACS can be used for the initial peak calling. However, when performing peak calling for ATAC-seq data, it is advised to adjust the default parameters so peaks are centered on ...
diffbind peak finding macs atac-seq macs2 written 21 months ago by igor20 • updated 14 months ago by YaGalbi20
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DESeq2 counts distribution across both genes and samples
... DESeq2 assumes negative binomial distribution for counts distribution. That refers to the distribution of counts for a single gene across all samples. What about distribution of counts of all genes across one sample? Each sample is normalized based on the geometric mean of all counts (or size facto ...
rnaseq deseq2 written 21 months ago by igor20 • updated 21 months ago by Michael Love17k

Latest awards to igor

Popular Question 11 months ago, created a question with more than 1,000 views. For DESeq2 with many samples
Popular Question 11 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 11 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 12 months ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 13 months ago, created a question with more than 1,000 views. For minfi MethylationEPIC errors
Supporter 2.3 years ago, voted at least 25 times.

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