User: msprindzhuk

gravatar for msprindzhuk
msprindzhuk20
Reputation:
20
Status:
New User
Location:
Last seen:
6 days, 10 hours ago
Joined:
2 months ago
Email:
m**********@mail.ru

Posts by msprindzhuk

<prev • 47 results • page 1 of 5 • next >
1
vote
0
answers
39
views
0
answers
How to program Galaxy pipeline to execute it on the new SRA identifier or on the uploaded FASTQ pair every new run?
... How to program Galaxy pipeline to execute it on the new SRA identifier or on the uploaded FASTQ pair every new run? We have a multistep pipeline from sra identifier to genome annotation, including many steps of data processing and normalization. The unsolved problem is how to make the first step of ...
stack pipeline sra fastq written 6 days ago by msprindzhuk20
2
votes
1
answer
38
views
1
answer
How to use and program Galaxy to download 300 SRA files at once form the NIH database?
... How to use and program Galaxy to download 300 SRA files at once form the NIH database? We need to get a large set of genome data for processing. We have tried to use sratoolkit and common file download manager for the aims of the batch download of SRA files. However, it could be a better solution to ...
sequences galaxy sra download written 6 days ago by msprindzhuk20 • updated 4 days ago by Mo Heydarian570
0
votes
0
answers
41
views
0
answers
How to get a .tab file with a list of mutated genes out of SNPEff in Galaxy cloud?
... How to get a .tab file with a list of mutated genes out of SNPEff in Galaxy cloud statistic HTML output? In History, can download only a HTML report (statistics output) with charts, when I go to the link with ,tab Gene file I get nothing. How to fix? ...
snpeff written 27 days ago by msprindzhuk20
0
votes
0
answers
62
views
0
answers
How to preprocess .fasta genome reference, .gff3 annotation file and the input VCF to escape from the Frame Zero error with SNPEff?
... How to preprocess .fasta genome reference, .gff3 annotation file and the input VCF to escape from the Frame Zero error with SNPEff? ...
snpeff vcf gff3 annotation fasta written 29 days ago by msprindzhuk20
0
votes
0
answers
35
views
0
answers
What does "WARNING: All frames are zero! " mean and how to fix it when using SNPEff?
... What does "WARNING: All frames are zero! " mean and how to fix it when using SNPEff? ...
snpeff vcf data software error gff written 4 weeks ago by msprindzhuk20
0
votes
0
answers
37
views
0
answers
When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis genome we have: WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found
... When running SNPEff on Galaxy on the normalized with VT tools VCF with M. Tuberculosis reference built-in genome we have: WARNING: Chromosome 'gi|559794742|gb|CP003248.2|' not found. File '/home/galaxy/galaxy/database/files/000/dataset_165.dat', line 34 WARNING: Chromosome 'gi|559794742|gb|CP003248 ...
input vt vcf snpeff written 4 weeks ago by msprindzhuk20
0
votes
0
answers
56
views
0
answers
What Galaxy tools can preprocess VCF file before running the SNPEff annotation process?
... What Galaxy tools can preprocess VCF file before running the SNPEff annotation process? We have tried VT Normalize. It does not help. What are the other ways to make VCF digestable to SNPEff? ...
snpeff postprocessing vcf vt preprocessing written 4 weeks ago by msprindzhuk20
0
votes
0
answers
33
views
0
answers
Are there Java, Ruby, R, and C# APIs, wrappers for Galaxy (like blend4php)?
... Are there Java, Ruby, R, and C# APIs, wrappers for Galaxy (like blend4php)? Is there any tutorial and some code examples on how to access Galaxy`s history programmatically to fetch a processed VCF file and postprocess it on a local computer? ...
remote access wrappers api written 4 weeks ago by msprindzhuk20
0
votes
0
answers
48
views
0
answers
How to filter genome annotation results to get a report focused on specific gene mutations (positions)?
... How to filter genome annotation results to get a report focused on specific gene mutations (positions)? What formats, functions, tools, software to use? The aim is to get a list of mutation profiles of the genes responsible for drug resistance. ...
filtering annotation report positions written 4 weeks ago by msprindzhuk20
0
votes
1
answer
44
views
1
answer
How to export computation results in Galaxy cloud?
... How to export computation results in Galaxy cloud? Is it possible programmatically and all-at-once manually? What are the options and is it written in docs anywhere? ...
export written 4 weeks ago by msprindzhuk20 • updated 4 weeks ago by Jennifer Hillman Jackson22k

Latest awards to msprindzhuk

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 80 users visited in the last hour