User: dk0319
dk0319 • 0
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Posts by dk0319
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... This is what I was looking for. Thank you ...
written 4 days ago by
dk0319 • 0
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... So that will give me the sequences containing a known DNA motif that I input. What I want, ideally, is to input a TF protein name and get a list of known DNA motif associated with said TF. ...
written 6 days ago by
dk0319 • 0
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... I have figured out how to extract fasta sequences from a bed file and then run motif discovery on it. Similarly, I have run my motif results in TOMTOM to identify proteins with similar motifs. But, I have yet to find a reliable way of searching for known DNA motifs by protein ID/name. What I want, i ...
written 6 days ago by
dk0319 • 0
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6 days ago by
Alex Reynolds ♦ 31k
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... Is there a work flow for generating the TPM from counts?
I am attempting to design a reporter construct using a list of significantly differentially expressed genes, but with consideration to the number of Transcripts that are present in in my control samples compared to my test samples. My hope is ...
written 9 days ago by
dk0319 • 0
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... I obtained gene counts in order to perform differential expression. Now I want to generate an MA plot comparing fold-change to RPKM. Is there a streamlined way to do this directly from a file containing gene id's and counts, without having to work with the bam file from which the counts were generat ...
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... Can anyone recommend tools for generating a list of genes that contain a DNA motif of interest. Ideally, one that provides a summary statistic. I was able to use MEME to identify a motif from several bed files. Now I would like to generate a list of genes with said motif preferably in the promoter ...
written 15 days ago by
dk0319 • 0
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14 days ago by
jared.andrews07 ♦ 7.9k
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... I was interested to know if bedtools can be used to retrieve gene names from multiple files that have shared peaks overlap. I am new to bedtools and I just wanted to confirm that this is indeed possible and if anyone can recommend any resources in addition to the manual. Cheers ...
written 5 weeks ago by
dk0319 • 0
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5 weeks ago by
Biological information research group of Harbin medical university daqing campus • 10
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... I have used commercial like CLC and snapgene in the past. As for free there is star, bowtie and Rsubread. But, I use those for RNA-seq not WGS. And none of them provide a visual map, apart from the commercial, at least as far as I know. ...
written 8 weeks ago by
dk0319 • 0
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... What are some of the popular free software tools for analyzing whole genome sequencing data? I am particularly interested in analyzing the sequences that map to a particular gene region in order to confirm predicted variation in the sequence. So if anyone as any recommendations, I am very interested ...
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... Unfortunately, I am limited to jupyter-lab at the moment, though I see your point. ...
written 10 weeks ago by
dk0319 • 0
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