User: Shelle

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Shelle0
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Posts by Shelle

<prev • 34 results • page 1 of 4 • next >
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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 24 days ago by Shelle0 • updated 24 days ago by h.mon20k
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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 26 days ago by Shelle0 • updated 25 days ago by Emily_Ensembl16k
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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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 5 weeks ago by Shelle0 • updated 4 weeks ago by Biostar ♦♦ 20
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Comment: C: Parsing header of FASTA File
... I tried this command and all the files go to haveNoChr.txt which is not correct as i have files with header (first line) as below: A few examples is as follows: >NZ_LS483492.1 Serratia rubidaea strain NCTC10848 genome assembly, chromosome: 1 >NC_013791.2 Bacillus pseudofirmus OF4, com ...
written 5 weeks ago by Shelle0
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Parsing header of FASTA File
... I have so many bacterial Refseq fasta files and want to parse the headers in the fasta files to see if is there any word 'chromosome' in the headers, as a side note there are some sequences in FASTA files started with '>' so i want to parse all the lines staring with '>' . I know i have files ...
fasta sequence header parse written 5 weeks ago by Shelle0 • updated 5 weeks ago by ATpoint7.9k
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How to download Refseq of bacteria as a COMPLETE genome format
... Can anyone tell me how i can download the **complete genome** format of **bacteria Refseq** from NCBI ? I mention complete genome as i don't want any word of **chromosome** be in the FASTA files. I just saw some post regarding this matter and it seems with the name of organism in the format of text ...
genome fasta refseq sequencing written 5 weeks ago by Shelle0 • updated 5 weeks ago by genomax57k

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