User: Shelle

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Shelle0
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Posts by Shelle

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Annotation of Single Cell Clusters
... Thanks for the information. Is there any other tool besides singleR which is not really dependent on Seurat? both of these tools are based on R and I would like to stay close to python because of downstream analysis ...
written 7 months ago by Shelle0
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Comment: C: Annotation of Single Cell Clusters
... Is there any list of universal marker genes that I can use? For example for 7 clusters in one dataset how I can know which one is representing which cell type marker genes? ...
written 7 months ago by Shelle0
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Annotation of Single Cell Clusters
... I am new to single cell. And I would appreciate guidance for my question I want to cluster a given single cell dataset for example PBMC. How can I annotate different clusters in the single cell without the knowledge of biology? I came across the scanpy but it was not useful and sounded like you nee ...
cluster rna-seq single cell tool written 7 months ago by Shelle0 • updated 3 months ago by Ashwini Patil20
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Map Gene names/IDs on Pathway with KEGG
... I want to map the list of gene IDs that i have to pathway and see if there is a pathway between the genes. I decided to go with KEGG using the code below to see what can be the name of nodes given the pathway id but for some reason in one line it gives me error so i am not able to run the code in th ...
pathway gene kegg written 2.2 years ago by Shelle0 • updated 2.2 years ago by h.mon31k
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How to convert Ensembl ID to NCBI ID
... Is there any tool or possibly a script that i can use to convert the long list of Ensembl IDs that i have to NCBI gene IDs? I would appreciate it if anyone give me ideas about this matter. ...
gene ncbi ensembl written 2.2 years ago by Shelle0 • updated 2.2 years ago by Emily_Ensembl21k
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Comment: C: Categorize sequences with biobloom tool
... same error as in my first response: Usage of paired end mode: BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [FILEPAIR1] [FILEPAIR2] or BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [PAIREDBAMSAM] ...
written 2.2 years ago by Shelle0
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Comment: C: Categorize sequences with biobloom tool
... I have to use all 19000 of bloom filters at one time. Array format was the only way that came to my mind. I even tried to slice the array so that not to use 19000 of filters but a bunch like 2000 filters and still the error "usage of paired end mode" like mentioned in first response. Array=(*.bf) ...
written 2.2 years ago by Shelle0
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Comment: C: Categorize sequences with biobloom tool
... I have tried to do it like below as well but the error is different and says "Argument is too long!" for the line starting with "biobloomcategorizer". I have only two files with fastq extension(_1.fastq _2.fastq) which is in a paired mode. And the number of .bf files is 19000. #! bin/bash A ...
written 2.2 years ago by Shelle0
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Comment: C: Categorize sequences with biobloom tool
... It is giving me this error: Usage of paired end mode: BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [FILEPAIR1] [FILEPAIR2] or BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [PAIREDBAMSAM] which i know biobloomcategorizer is working as i have tried not to write a for loop and j ...
written 2.2 years ago by Shelle0
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Categorize sequences with biobloom tool
... I am trying to use [biobloom tool](https://github.com/bcgsc/biobloom/blob/master/README.md#3-classifying-and-analyzing-sequences-with-biobloomcategorizer) to categorize sequences of sample that I have. I have to use one command like below: ./biobloomcategorizer -e –p /output/prefix –f "filter1. ...
genome sequence alignment software error written 2.2 years ago by Shelle0 • updated 2.2 years ago by Biostar ♦♦ 20

Latest awards to Shelle

Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to extract Refseq of downloaded files from NCBI
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to convert Ensembl ID to NCBI ID
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Alignment with BWA and SAMtools
Popular Question 2.2 years ago, created a question with more than 1,000 views. For download refseq of thousand of assembly file from NCBI

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