User: salamandra

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salamandra70
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Posts by salamandra

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Comment: C: How does MACS algorithm work on ATAC-seq data if there is no control sample and
... i have, and none of them seem to answer my questions, but as i'm no expert on bioinformatics is possible i am just not understanding what they are saying. ...
written 9 days ago by salamandra70
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How does MACS algorithm work on ATAC-seq data if there is no control sample and no model estimation?
... I understand that unlike for ChIP-seq, with ATAC-seq MACS doesn't estimate the model, which means it doesn't determine distance 'd' between the tags and therefore it doesn't shift the tags by d/2 in 3´direction (and that is why with ATAC-seq the --nomodel --shift 0 parameters are set). But if 'd' i ...
macs chip-seq written 9 days ago by salamandra70 • updated 9 days ago by ATPoint2.4k
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Comment: C: MACS for chip-seq: difference between sonication size(bandwidth) and fragment si
... got it. thank you very much! ...
written 9 days ago by salamandra70
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Comment: C: MACS for chip-seq: difference between sonication size(bandwidth) and fragment si
... I understand better now, thank you very much. But now have more two related questions:) - in that case why MACS don't also shift the tags from control samples? - Does we also need to shift tags in ATAC-seq, given the fact there is no protein binding there? ...
written 10 days ago by salamandra70
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ChIP-seq: Why MACS doesn't apply tag shifting to the control sample?
... If I understand right, MACS shifts chip-seq tags of a fragment into 3´end because the tags are just small sequences in the extremes of the fragment. But why does it only apply to the ChIP sample and not to the control samples (input DNA)? Or paired-end sequencing isn't done in control samples? Ref: ...
chip-seq written 10 days ago by salamandra70
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Comment: C: MACS for chip-seq: difference between sonication size(bandwidth) and fragment si
... thanks, but still have some difficulty in visualising this...May the watson and crick tags of the same fragment have different lengths? So what you are saying is that during chip-seq the DNA sequence where the transcription factor interacts isn't sequenced, only the flanking regions are sequenced ...
written 10 days ago by salamandra70
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MACS for chip-seq: difference between sonication size(bandwidth) and fragment size?
... In MACS algorithm article (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137) for chip-seq says: "Given a sonication size (bandwidth) and a high-confidence fold-enrichment (mfold), MACS slides 2bandwidth windows across the genome to find regions with tags more th ...
macs chip-seq written 10 days ago by salamandra70 • updated 10 days ago by ATPoint2.4k
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End coordinate bigger than chromosome size converting bedgraph to bigwig/ Setting macs2 chromosome size
... I used bedGraphToBigWig to convert the treat_qvalue.bdg file that macs2 outputs into a bigwig file. But it gives the error: End coordinate 92691 bigger than chr19_gl000208_random size of 92689 line 3066 of macs_chipvsinput_FOS_day2_treat_qvalue.bdg This happens because the coordinates th ...
chip-seq written 12 weeks ago by salamandra70 • updated 11 weeks ago by jared.andrews07280
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Comment: C: list in which each element is a vector of GO BP ids corresponding to an entrez g
... thank you very much! :) ...
written 4 months ago by salamandra70
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list in which each element is a vector of GO BP ids corresponding to an entrez gene
... I'm trying to retrieve a list in which each element is a vector of GO BP ids corresponding to an entrez gene. Then I plan to unlist those elements and do a unique vector with all available GO ids for BP only The following code: library(org.Hs.eg.db) xx.GO <- as.list(org.Hs.egGO) lapp ...
R lapply org.hs.eg.db written 4 months ago by salamandra70 • updated 10 weeks ago by Biostar ♦♦ 20

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Student 5 months ago, asked a question with at least 3 up-votes. For Install DESeq2 and edgeR with Anaconda

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