User: Artem Kiselev

gravatar for Artem Kiselev
Reputation:
20
Status:
New User
Location:
Russian Federation
Last seen:
1 month, 3 weeks ago
Joined:
5 years, 1 month ago
Email:
a*************@gmail.com

Posts by Artem Kiselev

<prev • 15 results • page 1 of 2 • next >
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Answer: A: How to access STAR index loaded into shared memory
... Your code for alignment would contain: --genomeLoad LoadAndKeep and --limitBAMsortRAM STAR --genomeLoad LoadAndExit --genomeDir $STARINDEX for file in $(ls myFastqs/); do STAR --runThreadN 5 \ --readFilesIn $file \ --outFilterMismatchNoverLmax 0.05 \ --alig ...
written 8 weeks ago by Artem Kiselev20
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Comment: C: How to run Snakemake pipeline from .py file instead of .smk file.
... Thank you, I described the problem very confusingly. The question was about dynamic writing of snakemake file, using python. ...
written 8 months ago by Artem Kiselev20
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Comment: C: How to run Snakemake pipeline from .py file instead of .smk file.
... Thanks for your comment, but it seems to me that it is more convenient to use a graphical interface for organizing scientific work, it is rather difficult to understand a large number of files, protocols and versions. With the help of KNIME, I have organized a very convenient pipeline for working wi ...
written 8 months ago by Artem Kiselev20
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Comment: C: How to run Snakemake pipeline from .py file instead of .smk file.
... My idea is the using of KNIME Analytics Platform for organisation of my SNP-calling pipeline, but despite the strong GUI capabilities, KNIME don't have enough good abilities for running of external programs (parallelism, etc). Inside of KNIME there is ability to run pure python scripts (form Knime g ...
written 8 months ago by Artem Kiselev20
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How to run Snakemake pipeline from .py file instead of .smk file.
... Hi, for my purpose I want to write snakemake rules as part of python (.py) execution file, how to do it right? Thanks! ...
python pipeline snakemake written 8 months ago by Artem Kiselev20
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How to use Snakemake with tools which don't have clearly defined output options for files?
... Hi, I would like to use Snakemake in my variant annotation pipeline. But Annovar don't have clearly defined file output option (I can assign only output folder and annovar going to attach to filename: "multianno.hg19), I can't describe final annovar output in "rule all", since it differs from the ou ...
next-gen pipeline snakemake sequencing written 12 months ago by Artem Kiselev20 • updated 12 months ago by WouterDeCoster40k
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Answer: A: Template-specific primers design
... I founded the tool for this task, PrimerWay, please use: https://github.com/zoldrax/primer-way ...
written 12 months ago by Artem Kiselev20
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Comment: C: Visualization of data obtained from target enrichment approach.
... Thank you for a concrete reply, now I began to understand that the main problem is not in visualization (there are many tools for that), but in the data preparation process. And the question is: using what methods and in what format should I convert my data so the result will be the information suit ...
written 5.0 years ago by Artem Kiselev20
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Comment: C: Visualization of data obtained from target enrichment approach.
... We really have specialized reporting software, where clinicists are working with NGS data, data are presented in tabular form (with the ability to simultaneously view in IGV). But we need the overall picture, we need to see what areas are enriched better or worse, which gene has more SNP, where we ...
written 5.0 years ago by Artem Kiselev20
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Visualization of data obtained from target enrichment approach.
... Dear all, I'm looking for tool or pipeline for visualization of NGS data obtained from target enrichment approach. Our custom panel consists of approximatly 100 genes, and I must find a way to visualize the result in an understandable for clinicist form. It seems to me that the most appropriate to ...
next-gen visualization circos snp written 5.0 years ago by Artem Kiselev20

Latest awards to Artem Kiselev

Popular Question 4.9 years ago, created a question with more than 1,000 views. For How to find positions of splice sites?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Template-specific primers design
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Visualization of data obtained from target enrichment approach.

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