User: grant.hovhannisyan

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Posts by grant.hovhannisyan

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Comment: C: GFF to BED
... For many of its tools, it can also work with gff/gtf files. See documentation pages for each individual tool. ...
written 22 hours ago by grant.hovhannisyan1.1k
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Comment: C: Merging fastq files
... If your fastq files are gzipped, you might need to use `zcat` instead of `cat`. ...
written 2 days ago by grant.hovhannisyan1.1k
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Comment: C: Acceptable duplication levels in ATAC-Seq data
... Is it a case of human genome? For a yeast with 12Mb genome I get around 55-65% of duplications with 30-40 mln reads, though I don't know whether its good or not. ...
written 6 days ago by grant.hovhannisyan1.1k
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Comment: C: motif search with ATACseq
... > Note that comparing across species is rife with issues. Yes, especially when they have 30% of genome divergence:) ...
written 9 days ago by grant.hovhannisyan1.1k
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Comment: C: motif search with ATACseq
... Hi Charles, the genome size is ca 12Mb and the ATACseq reps have around 20mln reads each (the coverage is much higher compared to human genome, though I don't really get what coverage in ATACseq context means). Regarding the replicates, for example I have used them in occupancy analysis with DiffBin ...
written 9 days ago by grant.hovhannisyan1.1k
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Comment: C: motif search with ATACseq
... Thank you Charles, very useful! One of the species I analyze is non-model, so I guess indeed there will be limitations. So either I will need to do motif discovery, or search based S. cerevisiae motifs. ...
written 9 days ago by grant.hovhannisyan1.1k
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Comment: C: motif search with ATACseq
... Thanks for input Devon! Regarding footprinting, do you think its fine to merge the ATACseq replicates to increase the depth (replicates are very reproducible)? Regarding the motifs, say I have found the motifs in the peaks, what kind of comparison between motifs of different species do you think ca ...
written 9 days ago by grant.hovhannisyan1.1k
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Comment: C: Error in HTSeq
... Not a solution, rather recommendation - better use featurecounts, faster and more flexible. ...
written 10 days ago by grant.hovhannisyan1.1k
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Answer: A: How many Mio reads are recommended for RNA-sequencing experiments in yeast?
... For doing DE analysis (on gene level!) with Candidas and Saccaromyces (genome size ~10-12 MB) we usually sequence 20-25 M reads, after mapping we usually get 90-95% of unique mapping, so the "effective" reads are around 17-20 mln (if you do trimming you also get rid of some data). If you only plan ...
written 10 days ago by grant.hovhannisyan1.1k
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motif search with ATACseq
... I have ATACseq data for two yeast species. I have called peaks with MACS2 and did occupancy and affinity analysis of peaks with DiffBind. Now I need to find motifs of TF binding sites in the peaks and compare those motifs between two species. There is a ton of softs and databases for doing the task ...
atacseq motif search written 10 days ago by grant.hovhannisyan1.1k • updated 10 days ago by Charles Warden5.5k

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Popular Question 1 day ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
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