User: cf556

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cf55610
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Posts by cf556

<prev • 12 results • page 1 of 2 • next >
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Pysam not giving samtools CLI
... I am trying to run velocyto but I am having some issues with samtools. Namely, I have installed pysam, but I am getting the following error when I try to run velocyto: FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools' Is there something more I have to do to get sam ...
python conda rna-seq written 8 weeks ago by cf55610
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Finding the right database for blast CLI
... 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 ...
blast written 4 months ago by cf55610
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Barnyard analysis advice
... 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 ...
barnyard R scrna rna-seq written 5 months ago by cf55610
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Comment: C: Creating a bedgraph
... Changing the extension worked. Thanks ...
written 11 months ago by cf55610
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Comment: A: Creating a bedgraph
... Changing the extension worked. Thanks! ...
written 11 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 11 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 11 months ago by cf55610 • updated 10 months 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 11 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 12 months ago by cf55610 • updated 12 months ago by Emily_Ensembl21k
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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 12 months ago by cf55610

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