Moderator: geek_y

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geek_y11k
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Barcelona
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geek_y
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8 years, 2 months ago
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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

<prev • 1,509 results • page 1 of 151 • next >
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Answer: A: Removing Unknown Batch Effects and Latent Confounders in Splicing PSI Data
... 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_y11k
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Answer: A: GNU Parallel Number of Possible Threads
... 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_y11k
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Comment: C: WGCNA Settings Help for RNA-Seq Data
... 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_y11k
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Comment: C: Looking for superfast heatmap algorithm
... [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_y11k
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Answer: A: gene expression correlation positive controls scRNAseq
... 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_y11k
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Comment: C: How to get a list of aligned read and reference positions using samtools
... samtools view in.bam “chr1:100-1000” ...
written 26 days ago by geek_y11k
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Answer: A: How to best summarize read counts overlapping promoters when read counts are def
... 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_y11k
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Answer: A: extract transcript sequence from bam file to know transcript length in control a
... 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_y11k
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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_y11k
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Answer: A: Do I have adapters in my reads?
... 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_y11k

Latest awards to geek_y

Scholar 26 days ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 4 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 4 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 5 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 5 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 6 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Great Question 3 months ago, created a question with more than 5,000 views. For Multisample VCF file to Structure file format ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 5 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 5 months ago, created an answer that has been accepted. For A: pdb to gff?
Great Question 5 months ago, created a question with more than 5,000 views. For Multisample VCF file to Structure file format ?
Scholar 6 months ago, created an answer that has been accepted. For A: pdb to gff?
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How get intervals of low coverage from a genome sequence?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 6 months ago, created an answer that has been accepted. For A: pdb to gff?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 6 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Great Question 7 months ago, created a question with more than 5,000 views. For Multisample VCF file to Structure file format ?
Scholar 7 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise

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