User: ofonov

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ofonov10
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Posts by ofonov

<prev • 8 results • page 1 of 1 • next >
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hap.py output variation
... I run hap.py twice on the same vcf file - first time without a stratification file, and second time with a stratification for GC and Low complexity regions. I am puzzled by variation in output of the tool, I get different values in precision and recall, for the same stratification category calculate ...
vcf hap.py giab ga4gh benchmarking written 4 months ago by ofonov10
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Answer: A: Which laptop will be good for most common and advanced bioinformatics works?
... Well, it really depends on the tasks you work with. Most of computationally intensive work is done on servers/clouds, with at least 64 Gb RAM and TBs of storage. E.g varinat calling pipeline on WGS can require 128 Gb of RAM, 16 cores and 5 TB of storage, while processing the data. On laptops some sm ...
written 23 months ago by ofonov10
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Comment: C: featurecounts of Rsubread strand specific orientation options
... Thanks for the link, it is helpful. ...
written 2.5 years ago by ofonov10
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featurecounts of Rsubread strand specific orientation options
... Hi, Featurecounts of Rsubread package has two options for stranded libraries: 1 (stranded) and 2 (reversely stranded). What is the difference between these two? How the reads should be orientated, which option on the attached picture corresponds to stranded and to reversely stranded? Fragment typ ...
strand specific featurecounts rsubread written 2.5 years ago by ofonov10 • updated 2.5 years ago by Carlo Yague4.6k
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Comment: C: Ensembl Genome annotations versions
... My concern was that if I used earlier version of the genome for the alignment, than the one on which the latest annotation was based, it might lead to some artefacts, since some features might have been moved due to the applied patches. Perhaps, I am overcomplicating things? ...
written 2.5 years ago by ofonov10
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Comment: C: Ensembl Genome annotations versions
... Thank you for the reply. Are Ensembl annotations based on the primary assembly (e.g GRCh37), or on the patched assemblies? Are there any difference between versions of annotation, except the updated features? ...
written 2.5 years ago by ofonov10
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DE on problematic miRNA data set
... I have a miRNA data set which looks somewhat not normal to me and I wanted to get an opinion of the community. The data set consist of 90 miRNA samples from cancer tissues. After trimming adapters and filtering by size (18-25 bp) by cutadapt there is very high variation of percentage of filtered ...
differential expression mirna written 3.2 years ago by ofonov10
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Sorted vs unsorted SAM/BAM
... Hi! I am quite new to NGS and could not find explanation of sorted and unsorted SAM/BAM files. How are these files sorted (what does SAMtool do to the file)? Why does it have to be done? Thanks! ...
bam samtools sam sort written 3.4 years ago by ofonov10 • updated 3.4 years ago by mastal5112.0k

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Popular Question 17 months ago, created a question with more than 1,000 views. For Sorted vs unsorted SAM/BAM
Popular Question 21 months ago, created a question with more than 1,000 views. For Sorted vs unsorted SAM/BAM

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