User: pacman

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pacman50
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Posts by pacman

<prev • 9 results • page 1 of 1 • next >
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How to Rename WDL/Cromwell output folders
... I start building a pipeline with WDL/Cromwell. Having an uninformative name for the output folder is troublesome, like using the hash # as ID for each runs. I was wondering if there is any build-in configuration/function for to let you rename the output folders. I have looked into the Cromwell, but ...
workflow cromwell pipeline ngs wdl written 8 weeks ago by pacman50
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Illuminate illuminate for NovaSeq
... I have python scripts that uses [invitae illuminate][1] module to parse and process the InterOP bin data. We recently switched to NovaSeq and unable to use invitae to parse the NovaSeq data. I was wondering if anyone has any experience to deal with that. I tried to use the illumina InterOP , but I ...
novaseq illumina next-gen interop written 15 months ago by pacman50 • updated 10 months ago by jfx31910
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Demultiplexing NovaSeq with samples having different sequencing cycles
... Our lab recently switched to NovaSeq from Hiseq which leads to having samples from multiple experiments sequenced with different read parameters in the same run. Right now, I make SampleSheet for every read parameters and run bcl2fastq for each of them which is both time and space consuming ( I hav ...
bcl2fastq written 22 months ago by pacman50
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Is BED file generated by bametobed sorted ?
... We use bamtobed to covert bam files to bed files. I am wondering if the output is sorted by default , because our output bed files seems to be sorted by chromosome and position. I am asking this question because we are using bedtools to calculate coverage with large bam files which takes up a lot ...
bedtools ngs bamtobed coverage sequencing written 2.3 years ago by pacman50 • updated 2.3 years ago by Alex Reynolds31k
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scRNA-seq: how to visualize SNN-Cliq clustering result
... I am comparing various clustering methods for scRNA-seq data. Does it make sense to show SNN-Cliq clustering result on a 2D tSNE plot? I am asking because one of the methods I am testing is kmean clustering of the PCA (which then use tSNE for visualization). A direct comparison between those two me ...
single-cell snn-cliq snn tsne scrnaseq written 3.5 years ago by pacman50
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How to use SPARQL to query OBO on Protege
... Hello, I have downloaded an ontology for chemical structure in OBO format ( [Classyfire][1]) , but I found it difficult to extract information on Protege by using SPARQL and SNAP-SPARQL. Some Annotations property has rdf and owl classes (e.g rdf:type owl:class), but most of them don't have one. I ...
obo rdf ontology sparql protege written 3.9 years ago by pacman50
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Comment: C: Batch Download from PubMed ftp server
... yes, it works, but not all PMC articles can be found on FTP server due to copyright issues :(  ...
written 5.3 years ago by pacman50
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Answer: A: Batch Download from PubMed ftp server
... Hi, I found a trick that make the process go a little bit faster.  1.) Find the corresponding PMC ID ( you can find it from PMC-ids.csv.gz)   2.) Follow the format of this URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMCXXXXXX/pdf -> this URL will re-direct the browser to the download link if ...
written 5.3 years ago by pacman50
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Batch Download from PubMed ftp server
... I have a list of articles (couple hundreds) that I would like to download the full text from PubMed central in PDF. Unfortunately, even though all of them can be found at PubMed central ,I can only download less than 10% of them from the FTP service ,based on the file_list.pdf.txt.  I am wondering i ...
ncibi pubmed written 5.3 years ago by pacman50 • updated 5.3 years ago by Danielson40

Latest awards to pacman

Popular Question 22 months ago, created a question with more than 1,000 views. For Batch Download from PubMed ftp server
Popular Question 22 months ago, created a question with more than 1,000 views. For scRNA-seq: how to visualize SNN-Cliq clustering result
Student 3.4 years ago, asked a question with at least 3 up-votes. For How to use SPARQL to query OBO on Protege
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Batch Download from PubMed ftp server

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