User: taraeicher

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taraeicher20
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20
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New User
Location:
National Institute for Advancing Translational Sciences
Twitter:
@EicherTara
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Last seen:
2 weeks, 3 days ago
Joined:
3 years, 6 months ago
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t*********@yahoo.com

Posts by taraeicher

<prev • 16 results • page 1 of 2 • next >
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Extract Pathway Topological Graphs (With Metabolites) from Reactome and WikiPathways
... I am looking for a way to extract pathway-specific graphs from Reactome and WikiPathways, including both genes and metabolites in the graph. My goal is to test a novel topological pathway enrichment analysis technique on these graphs. I'm looking for something analogous to what `KEGGgraph` does for ...
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Answer: A: Documentation for HotSpot Peak Caller
... I never found the documentation, but I did find that many people use the *broadpeak* option in MACS2 to call hotspots. It is then possible to obtain the total coverage of hotspots using the output file. For anyone else following this post, I would recommend MACS2 as a better option than HotSpot, as ...
written 11 months ago by taraeicher20
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Download Mass Spectra Given HMDB ID
... I would like to be able to query metabolites in batch by HMDB ID and download the curated mass spectra associated with these ID's (preferably from METLIN, but any other database containing mass spectra would also be fine). Note that I'm looking for the actual sequences of M/Z abundance values, not j ...
metabolomics mass spectrometry hmdb written 11 months ago by taraeicher20
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Comment: C: Documentation for HotSpot Peak Caller
... I want to verify that my DNase-seq assays meet ENCODE standards using the SPOT score: https://www.encodeproject.org/data-standards/dnase-seq/. To my knowledge, only HotSpot reports SPOT scores, but if anyone knows of another type of software for this purpose, that would be great. ...
written 12 months ago by taraeicher20
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Documentation for HotSpot Peak Caller
... This will probably seem like a silly question, but I would like to know if anyone has access to a current version of the HotSpot documentation. I am trying to run SPOT on a BAM file. I have checked the README from the HotSpot GitHub repo ( https://github.com/rthurman/hotspot/tree/master/hotspot-dist ...
peak calling documentation hotspot spot written 12 months ago by taraeicher20
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Answer: A: Obtain Full ClassyFire Ontology for Compound
... I wanted to note that, since this post, the Fiehn Lab has written a tool to allow batch classification, and this tool returns deeper levels of the ontology. It is available via a browser and, to my knowledge, no R package has been written yet: https://cfb.fiehnlab.ucdavis.edu/ ...
written 12 months ago by taraeicher20
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Answer: A: Pysam not finding mapped reads in BAM file
... After some investigating, I found that it was the index to the BAM file that was causing the problem. I generated this index using `bamtools index`. Given that this happened with several of my files which were indexed in this way, it looks like there may be a compatibility issue between my version o ...
written 14 months ago by taraeicher20
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Pysam not finding mapped reads in BAM file
... I have a BAM file with the following stats from samtools flagstat: 8022676 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 1336910 + 0 duplicates 8022676 + 0 mapped (100.00% : N/A) 8022676 + 0 paired in sequencing 4011338 + 0 read1 ...
chip-seq bam samtools pysam written 14 months ago by taraeicher20
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Obtain Full ClassyFire Ontology for Compound
... ClassyFire gives the option of inputting a list of InChI's or SMILES strings to obtain a classification: however, only the classification is given and not the full ChemOnt ontology for the compound. Is there any way to retrieve this ontology? Ultimately, I want to use it to compute similarity betwee ...
chemical similarity classyfire chemont written 20 months ago by taraeicher20
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Comment: C: Download Assembly Files from NCBI Genomes Site in Batch
... Hi, I just wanted to say thanks for the solution. This worked well. ...
written 3.0 years ago by taraeicher20

Latest awards to taraeicher

Popular Question 10 months ago, created a question with more than 1,000 views. For Algorithmic Difference between MACS and MACS2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Algorithmic Difference between MACS and MACS2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Download Assembly Files from NCBI Genomes Site in Batch

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