Moderator: geek_y
geek_y ♦ 11k
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I work with range of genomics data like transcriptome (RNA-Seq, scRNA-Seq, CAGE-Seq), open-chromatin/histone modifications/TF profiles, chromosome contact maps etc to understand tissue specific transcriptional regulation in human genome w.r.t to T2D.
I also work on small part of genetics (eQTLs, caQTLs, hQTLs etc) to understand role of common genetic variants in genome regulation.
Posts by geek_y
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... You can try [leafcutter][1] for differential splicing, where their model takes covariate information, which could be batches or first few principle components that might explain technical variation. Sorry, its not a direct answer to your question but a lot easier solution.
[1]: https://davidakn ...
written 8 days ago by
geek_y ♦ 11k
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... If you have 8 threads, run STAR without GNU parallel. GNU parallel meant to be used with commands that do not provide any parallelization. STAR already has that ability. ...
written 25 days ago by
geek_y ♦ 11k
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... How many genes are are you using ? Is it RNA-seq ? How many samples do you have ? How did you normalize your data ? ...
written 25 days ago by
geek_y ♦ 11k
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... [Fastcluster][1] , [flexclust][2]
[1]: https://cran.r-project.org/web/packages/fastcluster/index.html
[2]: https://cran.r-project.org/web/packages/flexclust/index.html ...
written 25 days ago by
geek_y ♦ 11k
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... In this paper, [Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data][1], *Nat Methods*, authors did generate loads of simulated data sets as ground truth. Their method allows to plugin any algorithms and let you asses your method.
You can access to th ...
written 26 days ago by
geek_y ♦ 11k
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... samtools view in.bam “chr1:100-1000” ...
written 26 days ago by
geek_y ♦ 11k
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... If two promoters overlap, there is no way you could resolve the data points from which promoter they came from unless you have a dataset with stranded and single base pair resolution.
One option is to assign the bins (regions of 100 bases) to both the overlapping promoters. Then get average read co ...
written 26 days ago by
geek_y ♦ 11k
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... If its about splicing, try [leafcutter][1] , [MAJIQ][2] or [rMATs][3] etc depending on your convenience to identify differentially spliced transcripts
[1]: http://davidaknowles.github.io/leafcutter/articles/Usage.html
[2]: https://majiq.biociphers.org/
[3]: http://rnaseq-mats.sourceforge.ne ...
written 26 days ago by
geek_y ♦ 11k
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Comment:
C: problem getting Seurat package
... Try installing Seurat from [conda][1]. Seurat has plenty of dependencies and its safe to use conda.
[1]: https://anaconda.org/bioconda/r-seurat ...
written 26 days ago by
geek_y ♦ 11k
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... Looks like your alignment file (bam) is truncated. `Premature end of file: /Users/tsopoulidis/bam_files/Finnley_et_al_mm9_UCSC/SRR4423430.fastqAligned.sortedByCoord.out.bam`
Can you run `samtools index` on it ?
The adapter sequence picard is showing is the default sequence that its going to use t ...
written 26 days ago by
geek_y ♦ 11k
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For A: Breaking down the reference genome chromosome-wise
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For A: Breaking down the reference genome chromosome-wise
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