User: cf556
cf556 • 10
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Posts by cf556
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... We are looking into the possibility of off-target mapping for some sequences that were added to our alignment reference. We are only concerned about off-target mapping to genes (including introns). We are also only concerned about off-target mapping in mouse.
To look at this I want to do a blast se ...
written 15 days ago by
cf556 • 10
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... I have a scRNA dataset with both human and mouse cells. Due to the upstream experiment, there is no way to physically separate the cells by species, nor is there a detectable fluorophore or another modification that could be used to isolate cells from one species or another.
I am wondering if there ...
written 9 weeks ago by
cf556 • 10
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Comment:
C: Creating a bedgraph
... Changing the extension worked. Thanks ...
written 7 months ago by
cf556 • 10
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Comment:
A: Creating a bedgraph
... Changing the extension worked. Thanks! ...
written 7 months ago by
cf556 • 10
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... 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 ...
written 7 months ago by
cf556 • 10
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... 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 ...
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... 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 ...
written 8 months ago by
cf556 • 10
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... Is there a way to convert from genome build to Ens.db version? (ex. grch38 -> EnsDb.Hsapiens.v87) ...
written 8 months ago by
cf556 • 10
• updated
8 months ago by
Emily_Ensembl ♦ 21k
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... 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? ...
written 8 months ago by
cf556 • 10
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... 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")
...
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