User: carlee.bettler

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Posts by carlee.bettler

<prev • 6 results • page 1 of 1 • next >
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How do I extract sequences to create a fasta file from an nhmmer .out file?
... I ran nhmmer to see if/where a certain gene was found in a fungi genome. The results of this query give me a .out file that contains multiple gene sequences that are part of a hit. However, the results of this hit are very unorganized. They are interspersed with other information about the alignme ...
fasta nhmmer alignment hmm hmmer written 4 weeks ago by carlee.bettler10 • updated 4 weeks ago by Fatima830
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HOMER tss command not working
... Hi, I'm new to working with HOMER and I'm trying to find binding at transcription start sites for mouse genome mm9 Chip-Seq data. Based on following the HOMER online manual at this link: http://homer.ucsd.edu/homer/ngs/quantification.html, my command is this: /HOMER/bin/annotatePeaks.pl sampl ...
homer chip-seq tss written 15 months ago by carlee.bettler10 • updated 15 months ago by Arup Ghosh2.7k
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Comment: C: MACS2 transcription start site analysis of .BAM files
... Thank you! Unfortunately I had to duplicate some research to get my .bam file that used mm9 :/ ...
written 15 months ago by carlee.bettler10
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Comment: C: How to convert Xena Browser normalized RSEM values to TPM values?
... Thank you for your response! ...
written 15 months ago by carlee.bettler10
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MACS2 transcription start site analysis of .BAM files
... Hi! I'm new to using MACS2 and I would love some help :) I have a .BAM file from an AF9 ChIP-Seq done with mouse (mm9 genome) cells. I'm trying to find binding sites -500 to +1kb from transcription start sites but I'm not sure how to do this. Do I need to provide a second file with TSS locations f ...
macs2 chip-seq tss written 15 months ago by carlee.bettler10 • updated 15 months ago by ATpoint41k
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How to convert Xena Browser normalized RSEM values to TPM values?
... When using the UCSC Xena Browser for gene expression (rna-seq) analysis, it shows the gene-level transcription estimates as a log2(x+1) transformed RSEM normalized count. Is there a way to convert these values into TPM values? What exactly are the units of these RSEM values? ...
xenabrowser tpm rna-seq written 18 months ago by carlee.bettler10 • updated 18 months ago by Charles Warden7.9k

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Popular Question 15 months ago, created a question with more than 1,000 views. For How to convert Xena Browser normalized RSEM values to TPM values?

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