User: msprindzhuk

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msprindzhuk40
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Posts by msprindzhuk

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Comment: C: How to annotate 500 vcf files using SNPEff or smth else and put every separate r
... explain, OK.................. ...
written 4 months ago by msprindzhuk40
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How to annotate 500 vcf files using SNPEff or smth else and put every separate result in a folder with the name of the SRA identifier?
... How to annotate 500 vcf files using SNPEff or smth else and put every separate result in a folder with the name of the SRA identifier? Is it implementable using Galaxy tools? ...
batch annotation snpeff written 4 months ago by msprindzhuk40 • updated 4 months ago by Guy Reeves1.0k
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How to align 500 fastq unpaired files to an uploaded reference and put every single result to a new folder?
... How to align separately 500 fastq unpaired files to an uploaded reference and put every single result to a new folder? Is it affordable to implement using galaxy tools? ...
alignment mapping batch fastq written 4 months ago by msprindzhuk40 • updated 4 months ago by Guy Reeves1.0k
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How to form a correct custom reference for making it acceptable by Galaxy variant callers?
... I have prepared custom reference made of 3 M. Tb. genes: >M. tuberculosis H37Rv|Rv0005|gyrB VAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAG YATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGL HGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVF ETTEYDFETVARRLQEMAFL ...
reference genome variant written 4 months ago by msprindzhuk40 • updated 4 months ago by Jennifer Hillman Jackson22k
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How to run preformed Galaxy pipeline programmatically and dynamically change pipeline`s parameters like new SRA identifier?
... How to run preformed Galaxy pipeline programmatically and dynamically change pipeline`s parameters like SRA identifier? Need to run a pipeline on an input of 500 new SRA identifiers. Is it possible using Bioblend, Python and Galaxy`s API? ...
batch pipeline api bioblend sra written 4 months ago by msprindzhuk40 • updated 4 months ago by Jennifer Hillman Jackson22k
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How to manage Galaxy memory resources programmatically using Bioblend and API?
... How to manage Galaxy memory resources programmatically using Bioblend and API? Are there any tutorials, cookbook, recipes for using Bioblend with Galaxy instance? ...
bioblend written 4 months ago by msprindzhuk40 • updated 4 months ago by Jennifer Hillman Jackson22k
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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 5 months ago by msprindzhuk40
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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 5 months ago by msprindzhuk40 • updated 5 months ago by Mo Heydarian790
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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 5 months ago by msprindzhuk40
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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 5 months ago by msprindzhuk40

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Rising Star 4 months ago, created 50 posts within first three months of joining.

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