User: mcsimenc

gravatar for mcsimenc
mcsimenc10
Reputation:
10
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New User
Location:
California, USA
Last seen:
3 days, 2 hours ago
Joined:
3 years, 9 months ago
Email:
m*******@gmail.com

Posts by mcsimenc

<prev • 9 results • page 1 of 1 • next >
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cellranger: min gene count and UMI/cell filter?
... I'm trying to re-analyze a 10x scRNA-seq dataset and follow the methods detailed in the associated publication ([main text][1] & [supplement][2]) but I have been unable to find the cellranger functionality they say they used: filtering cellranger aggr output by minimum number of genes per cell a ...
scrna-seq qc cellranger 10x genomics written 3 days ago by mcsimenc10 • updated 3 days ago by swbarnes28.9k
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Comment: C: NCBI SRA AWS AMI
... I'm having an issue with getting some fastqs that are only available in the cloud. If you go to: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR10620024 and click on the Data access tab, there are some aws s3 links in a section title Original format to files that I want. There are problems wi ...
written 4 weeks ago by mcsimenc10
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Comment: A: Salmon auxiliary output
... @Ahill I tried encoding these auxiliary files in ASCII format using the [base64 module][1] from Python and the resulting encoding is not what the file is described as containing in the salmon docs. For example, the `fld` file is documented as containing integer counts, but when I encode it as ASCII ...
written 3 months ago by mcsimenc10
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Tool or DB to find candidate transcription factors from promoter sequences? Arabidopsis
... Hi, I would like to take a promoter sequence and identify transcription factors which might bind it. Most tools and databases go the other way, identifying motifs from transcription factors. ...
transcription factor database promoter written 6 months ago by mcsimenc10 • updated 6 months ago by Alex Reynolds31k
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NCBI's tbl2asn for sequin files for GenBank submissions - what else does the program do in the system?
... Hello, I am making a MacOS GUI wrapper app for some of tbl2asn's functionality. The app is containerized a.k.a. sandboxed, which means it only has permission by default to read and write within the bounds of the app's space. tbl2asn runs successfully, as expected, from within the app when sandboxin ...
sandboxing tbl2asn genbank macos written 20 months ago by mcsimenc10
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Comment: A: Assembling PacBio reads using a reference genome
... Bump! Anyone know of any methods for the original question not listed here that may have shown up in the past 17 months? We are needing to assemble genomes from plant cultivars that are different from the cultivar for which 2nd/3rd round genome assemblies are publicly available. We are hoping to fi ...
written 21 months ago by mcsimenc10
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Where can I find GMAP? All links appear dead. Was the project abandoned?
... I want to use GMAP for my project, because Exonerate doesn't seem to be able to do multiprocessing/threading. I see the repo: https://github.com/juliangehring/GMAP-GSNAP has not been active and at the top states: *UNMAINTAINED and OUTDATED*: This was an inofficial archive of GMAP-GSNAP releases. Pl ...
gmap alignment gsnap software availability written 2.0 years ago by mcsimenc10 • updated 2.0 years ago by genomax91k
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Interpreting jmodeltest2 using transposon sequences results
... Dear Biostars community, I want to estimate divergence between two long terminal repeats from a single LTR retrotransposon, which are assumed to be identical when a new element is inserted. I have estimated substitutions per site this using baseml, selecting a model of sequence evolution more or le ...
model transposon jmodeltest2 long terminal repeats written 3.4 years ago by mcsimenc10 • updated 3 months ago by liangna199113140
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PASTEC repeat classification software (part of REPET) help needed
... I am trying to use [PASTEC][1] with my genomes on a cluster running TORQUE. The program's version of parallelization is splitting the input sequences in to batches and submitting many individual jobs to the cluster. I have not figured out how to (1) limit the number of jobs submitted or (2) increas ...
repet parallel repeat classification pastec torque written 3.8 years ago by mcsimenc10

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Popular Question 3 months ago, created a question with more than 1,000 views. For PASTEC repeat classification software (part of REPET) help needed

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