User: dk0319

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dk03190
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Posts by dk0319

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Tools for generating a list of known DNA binding motifs for a DNA binding protei
... This is what I was looking for. Thank you ...
written 4 days ago by dk03190
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Comment: C: Tools for identifying known DNA binding motifs for a protein
... 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 dk03190
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Tools for generating a list of known DNA binding motifs for a DNA binding protein
... 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 ...
chip-seq written 6 days ago by dk03190 • updated 6 days ago by Alex Reynolds31k
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Comment: C: Most efficient way to convert Counts to RPKM
... 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 dk03190
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Most efficient way to convert Counts to RPKM
... 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 ...
R rna-seq written 9 days ago by dk03190 • updated 9 days ago by ATpoint42k
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Tools for Discovering Genes Containing a DNA motif
... 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 ...
genome chip-seq written 15 days ago by dk03190 • updated 14 days ago by jared.andrews077.9k
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Using bedtools to identify genes that have overlapping chip-seq peaks
... 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 ...
bedtools chip-seq written 5 weeks ago by dk03190 • updated 5 weeks ago by Biological information research group of Harbin medical university daqing campus10
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Comment: C: Whole Genome Seq Analysis Software for Identifying Specific Gene Variants
... 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 dk03190
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Whole Genome Seq Analysis Software for Identifying Specific Gene Variants
... 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 ...
next-gen sequencing written 8 weeks ago by dk03190 • updated 8 weeks ago by swbarnes29.2k
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Comment: C: Issues with reading .bed files and compressing output in a specific format
... Unfortunately, I am limited to jupyter-lab at the moment, though I see your point. ...
written 10 weeks ago by dk03190

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