User: cf556

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cf55610
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Posts by cf556

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Comment: C: Creating a bedgraph
... Changing the extension worked. Thanks ...
written 3 months ago by cf55610
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Comment: A: Creating a bedgraph
... Changing the extension worked. Thanks! ...
written 3 months ago by cf55610
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Creating a bedgraph
... Hello, I have a file in bed format (chr, start, stop) and also a value associated with each peak. I would like to scale my peaks by the assigned value when viewing them in IGV. I was told bedgraph was the way to do this. I currently can get the peaks to appear in IGV but they have the values listed ...
atac-seq written 3 months ago by cf55610
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DEgenes bulk n = 2
... I have been spending a lot of time looking at scRNA seq and am now looking at some bulk data and have a few questions. Right now I am attempting to determine if a subset of known genes (32) are differentially expressed across two samples. I am not sure how to go about this considering I essentially ...
rna-seq written 4 months ago by cf55610 • updated 11 weeks ago by Biostar ♦♦ 20
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Parsing SAM output and comparison to IGV
... I am using the 10x possorted_bam.bam file to map edits in a gene of intrest. I isolated the SAM reads using `samtools view possorted_bam.bam | grep $gene_name > out.sam`. I then have been parsing the SAM file using a custom python script. When I go to The IGV coverage plot and hover over one the ...
sam rna-seq written 4 months ago by cf55610
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List of genome builds corresponding to ENS.Db versions
... Is there a way to convert from genome build to Ens.db version? (ex. grch38 -> EnsDb.Hsapiens.v87) ...
assembly ensembl written 4 months ago by cf55610 • updated 4 months ago by Emily_Ensembl20k
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Best JASPAR susbset for mouse
... I am looking at motif accessibility in mouse. Is the vertebrate collection (JASPAR) thought to be good enough for finding motifs, or should I try to subset by only human or mouse TFs? ...
jaspar atac written 4 months ago by cf55610
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Ascend runDESeq() not finding factors
... Hello, I am not sure if this is the best place to post this, but I figured here I have the best chance of getting an answer, currently I am trying to run ascend's runDESeq() function and am getting the following error. runDESeq(em.set, group = "cluster", parallel = FALSE, method = "pooled-CR") ...
deseq ascend rna-seq written 9 months ago by cf55610 • updated 8 months ago by Biostar ♦♦ 20
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KEGG profile convertId() returning coercion warnings, but having issues tracking down NA values
... I attempted to use KEGGprofile's convertId() to get my RNA-seq counts into NCBI gene IDs. I think the genes were given to me in mgi_symbol format. After running convertId() I revived the warning message, repeated until warnings() maxed out: 1: In FUN(newX[, i], ...) : NAs introduced by coercion ...
R bioconductor written 23 months ago by cf55610

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